So you are turning on the module first then booting up the PC? That is backwards. Normally you turn on the PC first, then go down your chain turning on each thing in order. It's quite normal for MIDI devices to send random bits of junk data when they boot up. For example I start up my PC, then power on my UW500, and lastly my MU2000. That is how a MIDI chain is meant to work. Either way though, you can just use the buttons on the Module to reset the unit after the junk data is received. I'd bet the X3MB is also getting the junk data, it just isn't reporting it you as it doesn't have a screen. In general most modules will just ignore data it doesn't understand, but Yamaha modules from the MU line will report it. Even with the Illegal Data message displayed, the module will still accept incoming MIDI and play everything it understands just fine.
Modules: CM-64, CM-500, SC-55MkII, SC-88 Pro, SY22, TG100, MU2000EX, PLG100-SG, PLG150-DR, PLG150-AN, SG01k, NS5R, GZ-50M, SN-U110-07, SN-U110-10, Pocket Studio 5, DreamBlaster S2, X2, McFly, E-Wave, QWave, CrystalBlaster C2, Yucatan FX, BeepBlaster