We did performance tests on the AL-88, it is able to support full-speed MIDI simultaneously on all of its ports. But... at MIDI speed each message takes around 1ms. So a chord takes around 4 or 5 ms. The human ear is able to distinct timing variations from around 10ms. So if you mix the musical stream with CC messages incoming from a not clamped controller (sending hundreds of messages per second), of course you'll feel something bad in the music. It's a common issue while merging computer controllers (virtual or USB) with hardware using MIDI cable. You don't have this issue using virtual instrument or using native CopperLan devices because they are not limited by the MIDI speed.
That said, this is only one explanation. It is also possible that the AL-88 is defective. To be sure, you can do the same experience using a simple USB-MIDI device.