I think I have the same problem on my 2002 Octavia Elegance TDI. The heater gets fairly hot when I am at a constant speed at decent revs, on the motorway for example. However when the car is stationary or stopping & starting the heater goes back to blowing otu cold air. This happens with or without the A/C engaged.
I doubt it's the mixer motor unless there's a chance it's opening and closing at random. I would have thought it's the water circulation, maybe an airlock. I'll have a search on how to bleed the system (unless someone can link me straight to it!)
p.s. Please don't reply "plug it into the diag machine." I'm sure this leads straight to the problem in 99% of cases but I don't have one and when I run out of DIY options I'll pay someone to have a look. Right now I'm skintypoos so I'd prefer to keep what money I have!