Never experimented something similar.
If you say this won't happen with other ROMs, the only thing which goes on my mind software-wise is phone is in huge activity, so it is consuming a lot of battery juice and, balancing discharge vs charge, phone charges slowly.
But if this is the case, you should have a hot device and a fast battery draining while not in charge.
Are you sure this is not hardware related?
Another cause of slow recharge, after the ones already mentioned (ruined battery...) can be a oxidated usb port. You could try using a contact cleaner spray and a little brush in the usb port.
No other ideas here