User level = newbie
To cut a long story short, I have a GM midi file with a number of tracks (Deep Purple, Child In Time) which were all playing through Microsoft GS Wavetable Synth. After some trouble I managed to get one of them to play though Kontakt Synth (the Hammond Organ sounds better) but now it's playing ahead of the beat and is out of sync with the other tracks.

What I've done:

• Open pre-made GM midi file in GTP4
• Add Instrument Track for Kontakt 5
• Set the output of the relevant midi track to Kontakt 5
• Play it - no sound
• Changed channel from 6 that it was on, to channel 1, seemed to work, I don't know why
• Switch off solo, so the other tracks can play
• It plays, but now it's out of time, playing just ahead of the beat. It was OK playing through MS GS. 

Any ideas anyone?

I think I've sussed it out now. 

I'm using the ASIO Cakewalk UA-1G USB audio interface. I've set up the Audio in GTP4 to use this, and I thought it was using this for everything. 

Turns out that Kontakt is using this, whilst the MS GS Wavetable is using the regular sound card. So I guess the regular sound device has greater audio latency than the ASIO device. 

So I guess MS GS Wavetable is behind the beat whilst Kontakt is on the beat, not ahead of it. 

I'm putting all the tracks through Kontakt now, which not only resolves the timing issue, but also sounds much better :-)

That is correct.
The MS Wavetable synth is technically an external device, and its sound processing is not subject to your latency setting in GTP4.
It's kind of a fluke, and best not to use it. You can unckeck it in Options>MIDI Devices, so it won't be available.
If you need a basic GM synth, you can use the included TTS-1.
It probably won't sound as good as Kontakt, but it's easy to work with.

That sounds like a good idea, but I'm not sure TTS-1 is included in GTP4, or if it is I can't find it. Can I download it? 
John

Rats. It appears that GTP4 is the only current Cakewalk offering that does not include TTS-1( aside from the LE versions which don't come with much of anything).
TTS-1 is not available as a download, and I have not found any reputable sources for another basic GM synth.
It looks like your best bet is to press forward with Kontakt at this point.