Ha...Ah, sorry. I'm the other person working on the project.
I guess he didn't explain it well enough. We've used XSE and another script editor, but the same problems occurred. In fact, we switched to A-Text because we thought it would alleviate the problem, but sadly it did not. I'm not sure what the offsets he used on A-Text were, but we did create our own scripts in XSE(using dynamic offsets if it matters), and usually assigned them to offsets such as 0x740000 and higher(or just let the dynamic do it for us), as I believe that's where the free space usually starts.
The main problem we had, actually, was that...say a script had multiple lines within it(such as any Trainer script and especially Gym Leader or important character scripts). Sometimes, the last or second-to-last line would overwrite the one before it, starting about 75% through that line.
Of course, we've had bigger bugs, like a script going haywire and turning into pure RAW coding and hex numbers, thus freezing the game when that person is conversed with. However, these are relatively simple to fix, as all it requires of one is to paste the original script back over the haywire one. For some reason this does not work with overwrites, and they simply reoccur.
Any help would be appreciated, but please do bear in mind that we HAVE used XSE and have created our own scripts, though it does not seem to help the problem.
It may just be a simple matter of the free space not starting at 0x740000, or there may be some over-complicated reason behind it.
