It's most likely from contamination somewhere in the process of conditioning and opaquing, as I'm sure you realize. Here's what I do to avoid the same thing:
First, I use specific finishing/grinding tools for each metal and I don't cross contaminate. When using stones, I only use aluminum oxide.
Second, I fiinsh my metal in one direction, never crossing over perpendicular to previous grindings , or reversing direction. This can fold metal over and cause bubbling later on.
When I'm finished conditioning, I hold the coping or bridge with hemostats and never touch the coping with anything again until at least after my second opaque layer. This is critical to avoid getting any contaminants, like oil from your skin on the framework.
Next, I sandblast the coping well with 50 micron aluminum oxide at 60 psi.
Next, I thoroughly clean the framework with high pressure steam. If it's a bridge framework, I place the framework in a clean, disposable cup of clean, distilled water for about 20 minutes in an ultrasonic.
After degassing, I sandblast at 50 psi for noble alloys and I don't for high noble alloys that have a light oxide layer.
I only use hemostats to hold the framework, remember!
I use paste opaque that is always kept covered to avoid getting dust particles in it, or if using powder opaque, only fresh opaque!
Then I pre-dry the framework (place on the firing peg and firing tray) on an electric hot plate. This dries the opaque from the inside out. It's most important for paste opaques.
If you follow all these steps consistently, you can eliminate your conditioning and opaquing procedure as the problem. If you continue to have these problems, you can assume that you have other problems such as dirt in your porcelain, or opaque, a bad, or contaminated muffle, or you are using incompatible metal/porcelain combination.
I hope this helps.