Are you using pitch bend or aftertouch? (You might be using aftertouch accidentally if you didn't turn it off.) If you have a lot of that information going across the MIDI wire, it will mess up the timing. Your sequencer should provide a way to thin or erase the control messages you don't need.

Are you using a Mac? Sometimes, the PatchBay program seems to lose the connection between timer ports. (There needs to be a connection between the hardware and the sequencer.) You just need to redraw it.