Nickk..without actually taking a look or getting more details, it will be hard to say. As you may know, some of those files/folders/scripts should be setup with 444, 644, 755 and 777 permissions, and they must be ftp'd a certain way (ASCII or Binary). It is a nightmare doing all this manually and if done wrong, that may pose a problem.
For instance, a client used my auto-installer and experienced an issue like yours and it ran us both crazy trying to find the issue. It turned out requiring an adjustment in the code and the script execution time out on the server, as the script simply stopped executing after a certain time, giving him less pages than he was supposed to get (it was a HUGE project).
After making an allowance for a longer execution time and an adjustment in the script, everything works perfectly for him now.
So I guess what I am saying is that without actually going into the server or getting specific details (that you may not want to disclose), it is going to be difficult for someone to pinpoint exactly what may be happening.
You may get 50 answers to this and they could all be wrong. If it is not a permission, ftp upload method you used with the scripts or a server execution (timeout) issue, then it is going to be difficult to say what else it could be without actually looking into the server or the logs to determine what causes this problem for you.
Sorry I could not be of more help.
Hope you find the issue and work it out. It's well worth it to keep at it until you solve it though.