I'm experiencing similar problems with Get in Norway (previously owned by UPC) with recent builds.
Tvheadend lists a lot of services on wrong mux, in addition to the correct mux. Because of this, lots of services are listed twice. Hence, only one of those services actually works.
Example:
Mux1 actually contains:
MTV
Eurosport
Mux2 actually contains:
Discovery
History channel
But tvheadend could list them like this:
Mux1:
MTV
Eurosport
Discovery
History channels
Mux2:
Discovery
History channel
Tvheadend lists Discovery and History channel on both muxes, but ofc they do not work on mux1 as they are actually on mux2.
When using an older build of Tvheadend (currently using one from 31/12/2012), it works as it should, with all services found on the correct mux.
I hope this explains my problem in a way that is understandable. Could this be the same problem you are experiencing?