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I have been there in summer and my wife has been there out of season slightly.  I would have though you would be OK in September, but as someone has said, you can get storms in the mountains.  They are geared up for winter (ski-ing) holidays rather than much in the summer - everything is closed 12.00 to 14.00 and I mean everything, except the odd bar tobbac, and the two supermarkets serving the French side of the border with almost duty free fags and booze, if they don't get caught.  (It isn't in the EU - so check your insurance covers it.) 

September normally is good weather in the Pyrenees and of course you may have an afternoon or evening thunderstorms, as such is mountain climate. But, apart from the weatherforecast, this usually can easily be recognized from the type of clouds and number (1 is OK, two or three of those very high towering ones usually means thunder to be expected as from about three o'clock six or seven o'clock, sometimes later in the evening) and speed of development of them. Normal rythm for this is three or four days of very warm weather building up air instability, and the fourth, fifth or sixth day an afternoon/evening of rain.

Do peg your tent well, use all guy ropes, as the evening thunder may be accompanied by a very sudden hard 'falling' wind ghust. This way your tent will be safe also in your absence, e.g. when walking, or when sleeping.
I experienced this when i was near Luz St. Sauveur (actually St Bazerque, just a bit further towards Gavarnie), and I must say I felt good, especially when being safe and warm myself, we could have a nice hot cup of coffe, while others who recognizably had not pegged down and guyed well were re-pitching their tents, and by the way, still had fun.

The advantage of staying on altitudes of 800 or 1000 mtrs  is that the nights are a bit cooler for sleeping, while day temperatures are nice and warm.

On the whole: very nice weather, beautiful area, but do prepare for one thunderstorm with hailstones once a week or once every two weeks. On those days (visible) go on tour early and be back at about two or three o'clock. When driving around of course no specific time to return, but get of the mountain before two. Or better, do something else like visiting a cave.
Nice walks in and around the valley of Luz St Sauveur and towards Gavarnie: standard of course the Cirque de Gavarnie, but certainly too the Cirque du Troumouse (less touristic, very peculiar landscape), the Brèche de Rolland (Brèche actually forms the border with Spain). If you prefer a ski lift to do the first ascent: Pont dÉspagne qualifies well too.
And if you choose to stay in the valley of Ax Le Thermes, apart from beautiful walks, visit one or two caves with prehistoric paintings. There are several, one of which actually is a walk into the mountain with torches and a whole wall of pantings at the very end. This one should be booked a few days in advance, due to the limited number of visitors, don't know the name anymore, but drive from Argeles Gazost toward the Plateau de Beille, in the beginning of that valley left halfway up the slope, signposted. Entrance is a large cave halfway the mountain. Date: about 18.000 BC.

> a serious mountain walk <
As far as I am concerned all walks in that area are serious. But the walk is one that can be done in a very reasonable time. It still is a walk (a beautiful one), a good walk as I hink the ascent is about 500 or 600 mtrs counting from the highest parking lot where the real path starts), but no climb. But every walk where the ascent amounts to more than 200 or 300 mtrs in this type of areas must be taken seriously as to condition and outfilt. No sneakers as shoes, enough clothing, incl spare and rain clothing, sweater, enough drinking water etc.
Only very low walks can stand easier outfit, shoes. But I can't imagine that someone interested in visiting the Pyrenees only wishes to walk half an hour along the Ariège (done some nice canoeing by the way).
But maybe that assumption is totally wrong.
Lack of being prepared does happen. I met some young people up at the mountain hut at the Brèche de Roland in shorts and sneakers. Of course we/they got a serious shower and hailstones making everything rather slippery and cold: we guided them back untill the were on the easier path again... They decided to buy better shoes next day and also bring long trousers, a sweater and rainproofs for their next walk, even if a lower and more modest one.
I think we are no hikers but reasonable walkers.

By the way, when choosing the Ax les Thermes valley, driving up to the plateau of Montaillou (the Cathar village of which the archives have been researched) and doing a walk up there is nice too. Easier walks up there and still rather high in the mountains. Good maps needed.

at Jim: As to fear of thunder: stay low when clouds are of the towering cauliflower headed type. Normally no clouds or normal light clouds of the non-cailiflower type are OK. Specifically the cauliflower heads indicate strung 'unrest', thermics movements, which after some time often end in thunder. Again only after a few days.
If you know this rule you will be safe and your girlfriend does not have to fear anything. These things are valid for all mountains areas.
The nice thing about France is that in bookshops there usually are booklets for sale with well marked walks. Especially the series of Chamina, but unfortunately that organisation specialises in other areas. I had some other good booklet for the Pyrenees and always buy good walking maps (1:25.000) and always keep track of where I am. One should reads these maps (pref. IGN maps) well, e.g. heights, type of forest, landmarks, shed. All are indicated and give you control.
In mountainous areas calculate a speed of 3 kms per hour walking plus one hour for every 300 mtrs ascent. This gives you a very good indication of the duration of walks. Plan the first walk not longer than two hours and see how you do.
Better take the good tips now even if they suggests that this type of areas are dangerous, and look through them. A well prepared person remains safe and enjoys the mountains. I had to make some mistakes as I never got the tips in time. Can you imagine walking/climbing Muckish Mountin in Donegal Ireland during rain with sneakers?!  That taught me the importance and comfort of good shoes, especially remembering descending the scree slope as we missed the proper path by the fog. Ouch, my ankles were totally scratched.
And remembering an undercooled wife who refused rain trousers and on purpose left them in the car without me noticing it as we departed for a 3 1/2 hour walk at 24 degrees C. and were surprised by snow (in November in Auvergne, we should have known that very warm sun and snow covering the marks of the walk may happen on one day, good maps fortunately and good sense for direction and position brought us back safely, including driving back via the pass in the snow, but my ex-wife had to do a lot of warming up, as she also refused my rain trousers, fearing that her knee might lock when we would stop).
So we'd better scare you and your girl friend a bit now so that in the end you will experience only the joys...