Thanks for the response mate.
I used to have the following setup and noticed the same that intermittantly fans would stop reporting to the Aquasuite software:
AE5 PRo
3 x Scythe GT's on Fan 2
1 x MCP-355 pump reporting connector on Fan 1
I now have the following:
AE5 LT
2 x Akasa Apaches (140mm) on Fan 4 (RPM controlled)
1 x Coolermaster flow 200mm on Fan 2
1 x MCP-355 pump (This is a different pump to the one I used previously) reporting connector on Fan 1
Fan 1 shows no reading at all (so I can't see what RPM's the pump is spinning at). It did at first but unlike my previous setup which used to be intermittant this now shows no reading at all
I'll try the things you suggested anyway mate. Thanks - at least someone is willing to help!!