When I place the constant gain or power transistion over into the middle of 2 clips to join them, the effect (highlights as a dark red/brown colour) refuses to 'sit' between the clips and insteads defaults to the end of one audio clip or the start of the next one. This is on the timeline. On some clips it will join them together, on others it wont. What am I doing wrong? thank you

Ref: Adobe Premiere Pro * Transition overview: applying transitions (http://help.adobe.com/en_US/premierepro/cs/using/WSE2A9B838-1422-4d8a-9A03-CFDF4332533B.html#WS17A423FB-FEF8-4172-A7C8-8521D8CCB8C8)

I believe it's because the 1st clip has no handle (frames after the out point) for the transition to fade out. So if your sequence is set to 30fps and you have a transition of 1 second, the 1st clip needs to have at least 15 frames beyond the end of it (out point) for the transition to have an affect. Otherwise it will just snap to the end of the 1st clip and fade out the last 30 frames. I hope that makes sense, I was confused the first 3 times I read it.

A second possibility is that the two clips have a small gap between them. Zoom in to the timeline to check for this. If the gap is only one or two frames it will not show at the sort of zoom level you use for editing.

Click on the transition and open the Effect Controls.
There you will see why the transition is placed like it is.