Found the source of the problem I believe, as I suspected it was a problem with the messages being displayed, thus 2 birds were fixed with 1 stone.
I had to fix up the look because it was seriously bugging me out to stare at all that code without having a clear guide. I will be continuing to clean up the rest of my map file, and if you would like I can submit it to you, that way an easier version for scripters is available.
Anyway the problem I believe was when the messages were created the process continually concatenated the string, so that pieces were missing and/or cut out. Which could easily cause things to be displayed in less than desirable locations. The reason it was a problem in Linux is as I said before, the libraries for string work may be much more strict than windows libraries.
I have had my test server up for 3 maps straight, been in and out testing it, and its been rock solid. Seems like that was the only problem area, besides the mapvault.dat not loading on a mapchange (well not loading at all hehe).
I may have a better way to get the values from mapvault.dat as well, I will post if I get it working so that people don't have to define variables in their amxx.cfg file.
Anyways, that's my happy news of the morning, now off to bed hehe...