It sounds like the joint compound is partially drying before the tape goes on.
It might be that you are too slow putting the tape on after you have spread the joint compound along the seam. If the compound starts to dry a bit then the paper tape doesn't stick properly and will bubble up later on.
You can stop this by doing the seam in shorter sections so it doesn't dry as much. (which is what I did)
The experts tape a long seam in about 60 seconds flat so drying is not a problem. It looks real easy but it's like everything else in life, it's only easy if you do it every day.
Apparently you can also wet the tape first but I didn't try this so I don't know how effective that is.
For big jobs it's probably best to put up the gyprock yourself but then get in a real person to tape the joints. They do it fast so it doesn't cost much and the job looks far better.