Windows 7: Merged channels stop working, but both tuners work ok

I have been running media center for 3-4 years and relatively recently have had this trouble.

I have a freeview tuner (a relatively old Blackgold tuner referred to as "signature" on their website) and a DVB-S2 satellite card from hauppage.

The channels have always worked ok, but 2-3 months ago the satellite version of the channels seemed to stop working.

I recently reset the TV database by using the Hack7 tips method, and re-tuned both tuners from scratch. I then went through a lengthy 3 hour process to merge all the channels I needed to merge, so I can watch on one tuner and record on the other.

This all worked fine at the time, however within a day, all the merged channels had stopped working...with the exception of ITV which was merged but carried on working fine.

Channels that were satellite only, worked fine.

I then split the merged channels, and now the freeview version of each channel works perfectly (even though it wouldn't when merged), whilst the freesat version refuses to work - even though the channels that were satellite only, still work quite happily.

So both cards are ok and working, just not when they are merged together.

Any tips on how to investigate this further or what else to try?

I am trying to avoid reinstalling Win 7 and then another 3 hours of channel searching on top....