Right, bit of an update, although I think it'll only muddy the waters.
I installed 3.0.1 last night and it seemed to be working fine; none of the problems other users on here had mentioned. I had a bit of a play with the new delays and a general fiddle, all was working well, bar the afformentioned different sounding patches. Both patch windows were working fine (I used them to merge the entries for the competion without a problem).
Tonight, trying to investigate this problem further, I couldn't recreate it: It sounded identical to the 2.7.5 version. To make matters worse, whilst trying to capture the way it had been sounding yesterday, I stupidly managed to overwrite the different-sounding OS3.0.1.wav with one that whilst rendered in 3.0.1 sounded identical to 2.7.5. At this point I was starting to think I'd imagined the whole thing. I tried loading up Live and the Virus again and double checked everything. I couldn't see anything I'd done differently, but this time it once again it sounded different to the 2.7.5 version; it sounded "new" again, exactly like it did last night!
When I attempted to bounce this to a .wav, the virus appeared to crash- the high pitched whine/drone other users reported started as well as a host of other problems I'd seen detailed here: second pane of the patch browser froze and just overwrote the upper pane, etc. I have just reloaded it all again (once again, not doing anything odd) and it all works fine, but sounds like the "different" version of the patch again!
I should emphasise I'm not using a usb hub/getting any errors and that I never had a single hitch during the dozens of hours I've run 2.7.5.
So, in summary there appear to be at least 3 states it operates in and appears to switch between at random:
1. Sounds like 2.7.5. All functions tested work fine.
2. Sounds "new". All functions I tested work fine.
3. Sounds like 2.7.5. Some functions don't work/it crashes out entirely resulting in a high pitched squeal that sounds like a feedback loop.
I will investigate this further tomorrow and post my findings. I do testing of programs as part of my day job, so hopefully should be able to at least come to some logical conclusion, even if that is that it does seem to randomly switch between the 3 states on startup!