Hi Matt, thanks for the response!
Yes, I am using MIDI cables. The MIDI Interface connects to the computer via USB, and the keyboard connects to the interface via standard MIDI cables.
The timing problem was a guess; when I look through the Roland manual for my keyboard I see that on at least one message they recommend that you "rest" after sending it, so I thought perhaps with the new gear it might be some kind of race problem.
But it turns out the problem wasn't timing at all. It looks like I had some of my sysex messages mis-configured and the keyboard was just ignoring them. I'm stumped as to why they did work before (I.E., the same mis-configured messages worked fine with my old computer and MIDI interface), but once I realized the goof I was able to regenerate the sysex files with the correctly formatted messages and it all seems to be fine now - the messages all seem to be recognized and responded to.