I'm not familiar with RSLogix 5 but I have seen this problem before in 500. What happens is that somewhere along the line, somebody does an upload from the PLC into a new file which gets saved in the programs directory (no documentation). Meanwhile, the offline file you want to use (with documentation) somehow gets tweaked so that the checksum of the file no longer matches what's in the PLC. Even if you have this file open when you try to go online, the software sees that it doesn't match so it automatically searches the program directory and voila, it finds the copy with no documentation and goes online with that one. The only way to solve this is to either merge the documentation from one file to another, or download the documented file and overwrite what's in the PLC.
Again, this is my experience with RSLogix 500 and I don't know how similar RSLogix 5 is in this regard.
EDIT: To quickly check whether this is happening, look at the filename in the title bar before and after you go online--they should be the same.