I used to use iPod Manager [1].
When you add songs, do it from the original firmware. With the iFlash and all that, transferring files while loaded into Rockbox will cause the issue you mentioned... a lesson I learned after transferring about 80gb of FLACs.
When you boot the iPod, lock it right away and it'll boot to the normal firmware. The transfer speeds are better than using disk mode.
https://www.foobar2000.org/components/view/foo_dop