It's probably a bug in NFL2k5Tool.
NFL2K5Tool only really works well with the base Roster & franchise files right now (for saving data).
I thought it generally read data well, but it has bugs for sure.
The best way to accomplish the task of replacing teams in a file would be the following process:
1. With NFL2K5Tool, open Capa's file; List Contents; save contents in a text file.
2. Get the Text data of the Teams you want to add.
3. Make a text file with all the data you want to apply (Ideally sort the players best to worst by position or try the sort operation under Edit->Sort Players)
4. 'Load Save' use the Base Franchise (or base roster)
5. File -> 'Apply Data without Saving'
6. Edit -> 'Auto update Depth Chart'
7. Click 'Save'; save as a new file.
If you open the File with Finn's editor after you edit it with NFL2K5Tool, do not let it auto-correct anything if it prompts you.
If it's still giving you trouble, upload the text you'd like to apply (specify roster or franchise) and I'll take a look.