Dmtri, again thanks for your offer, but I am coming back to the conclusion that this is not directly a problem with MegaDrum. I think it is a USB compatibility issue since I don't see the sysex timeouts on systems with more recent Intel chipsets. I now realize that all of the systems that have sysex timeouts use the Intel ICH9 southbridge (aka "Mobile Intel 4 Series Express Chipset Family").
Here's what I discovered today: The Intel Series 4 Mobile chipset uses a rate-matching USB hub. When MegaDrum is plugged directly to the USB port, it is routed to the USB 1.0 controller. When connected through the passive hub, it is routed through the USB 2.0 controller. I stumbled on bug reports that state that USB sound cards will have performance issues with these chipsets when routed through a USB 1.0 controller, so the problem with MegaDrum sysex may be related to this bug. I believe that my other USB sound and MIDI devices are all USB 2.0, so they don't have issues on these computers.
I'll be able to dig into this further today.