The fix for this, if anyone else was wondering was to delete all my preferences for logic from library/preferences. A corrupt plist file was causing the BSP to not show up as a midi port destination.
HOWEVER, while I can now send midi from an external midi channel in Logic to the BSP and record the pattern in the BSP. It is not without issue - it seems to get stuck on the last note played for the SEQs, most of the time keeping the note duration information. The step length is correct in the BSP too. Which is weird. Additionally, the DRUMS pattern always seem to add extra steps, despite the midi going into the BSP being 100% quantised to the correct 16th note duration. I'm wondering if this is a latency issue going in, and the BSP is quantising the input across two steps?
Occasionally the recorded midi in the BSP also shows ghost notes - short notes that are chromatic, next to the original note in. These don't always happen, seems to occur every 5~ recordings or so.