
What custom format are you using for each FileBot instance?

The screenshot above suggests that you have configured different a
custom format for each portable FileBot instance, this generating different file names. Matching works fine, since each file / episode match is correct. Naming is working as configured, and can be configured differently as required.

Note that each portable FileBot folder has its own portable settings in that folder as well. You can transfer your settings, including custom formats, from one FileBot instance to another via
Backup and Restore Settings.