That's supposed to be supported per
this doc. So if nothing else you can file a case.
Is the custom segment visible on the JE form that Amortization schedules are using? Also, do you have the custom segment exposed to JE lines in general via the segment setup?
I believe it was mostly around reporting, but there used to be some weird issues that would occur if you didn't have it set up to be used on JEs. So I got used to just setting it up to be on JEs and then hiding the field off the form if I truly didn't need it on JEs.