Since it still looks like text from at least one server, I assume the file isn't actually being changed. Confirm this with the file modification date/time.
Try running [tt]cksum[/tt] on the file from each system. This gives a checksum of the contents of the file. This will let you know if the file is actually the same, or different.
If the [tt]cksum[/tt] command shows the same numbers, then it's how the file is being interpreted or displayed that's different.
I would first start by looking at mount options. Maybe the filesystem is being mounted on one system in a way that the file isn't being seen properly.
Check the file with [tt]cat[/tt]'s "[tt]-vet[/tt]" options ([tt]man cat[/tt]). This will show unprintable characters. It's possible your terminal/session settings on one system cause binary characters to be displayed on one system, but ignored on another.
Check the file with [tt]od[/tt] on both systems. Again, this will show you what's really in the file. This will let you know if the difference is a real difference between systems, or that they are just displaying differently.
Last would check for differences in your sessions' [tt]stty[/tt] settings, terminal program settings (putty?), environment settings, and anything else that could be affecting how the terminal program is interpreting characters. [tt]cat[/tt] just throws the file to the attached terminal. Differences in terminal settings can change how that file is displayed.
Have you tried making a local copy of the file and checking it?