Are you trying to control GB's software instruments with MIDI continuous controllers such as control numbers 0 through 127 (bank select, portamento, legato, etc.) or channel mode or voice messages? Here are some quotations from page 104 of the David Pogue book GarageBand 2: The Missing Manual:
"...GarageBand only records, displays, and edits streams of MIDI information like pitch bend, key velocity, and pedaling."
"Professional music software can record and play back dozens of other kinds of invisible MIDI data."
"GarageBand doesn't record or let you edit these MIDI data types (not that most GarageBand musicians would even care)."
These kinds of MIDI continuous controllers would only be available with software like Logic Express or Pro or perhaps third-party AU plug-in instruments (VSTI's) in GarageBand.