IDK if any of the changes would affect the colour mode issue, but there have been some extensive fixes since 4.2...
http://liballeg.org/stabledocs/en/changes.html
It's hard to know what positive benefits we'd gain from there, but there are some critical fixes in there that necessitate updating. Furthermore, at least some touchscreen support was added, as was the ability to compile for the PSP, which would probably be a very attractive option for ZC, although I'm uncertain if the PSP has enough RAM to run ZC (unless we fix ffc/map memory usage).
There are many *nix based fixes, and some OSX fixes. I'm unsure what 'Added Windows 7 detection' and many of the other fixes are meant to imply though, as many of them are vague.
There's really no immediate-apparent reason not to update to 4.4.2, so I think it'd be good to try it, and see what breaks (if anything).
I'm a bit confused on one thing: I've also seen a package 'Allegro 4.9'. Do you have know anything about that? It seems to predate 4.4, which leads me to believe that it was a dev-cycle ID for ag5 alphas, or something.
Edit: Confirmed. Allegro 4.9 was early ag5.