I might be entirely wrong, but this sounds as if you literally placed your hacks from your Bon Voyage downloads folder into your Free Time downloads folder. If you've done this, then I know what your problem is. Many FFS hacks have been updated so you shouldn't use the copy you had before in FT. You should download a fresh copy from the hack directory. If I have misunderstood your post then I'm sorry for wasting your time with this explanation.
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Well, I did and I didn't. I have a number of non-awesome hacks which haven't been updated for the last couple EPs. They've worked fine to date, so I put them in one or two at a time and started the game to see what happened. Dangerous, I know, but it seemed fine at first. I might have missed a newer one, or simply didn't check thoroughly enough. Anyway, I took everything out (again) and went through again. This time I didn't put the older hacks back in. Instead I used some TwoJeffs hacks (ACR) and some Awesome hacks that do similar things. I'm still trying to find documentation for one of the extras from TJ's Director's Cut, because it looks like a good replacement for one of the old hacks, but I don't know for sure what it does. There are still some I need to check again too, that were made for Seasons. I haven't seen updates yet, but as far as I know Free Time didn't change how gardening worked so they're probably ok.
This does go to show how many modders have left the Sims2 community though. Their hacks go un-updated, and some of them were useful. A lot of them can be replaced if you look around long enough, but the replacements I'm finding often add functions I wasn't sure I wanted to add. Oh well.