I have some further information to provide in this.
I just finished migrating another box from Gentoo to Ubuntu 6.10 and ran into the exact same troubles as previously with other Ubuntu 6.06 boxes. I didn't change any hardware configuration (or for that matter the location of the transmitter itself on a receiver). The serial transmitter worked perfectly in Gentoo, and stopped sending functional signals for Edgy. I grabbed a newer snapshot that included support for MCEUSB2 transmitting and tested with a MCEUSB2 transmitter. To my surprise, it worked out fine. It appears to be problem that only plagues the serial transmitting module.