I dont have any coupling or filters installed.
It is a miracle that you can control "ALL" with no phase to phase coupling. But miracles happen.
To help us try this: Pick one of your X10 outlets you can not control, and plug one of the X10 plug-in modules that IS working in to the uncontrolled outlet on the unresponsive X10 outlet. Does the plug-in module still work? If it does not, it could help explain a few things.
I had a house in Florida which had all the lighting fixtures wired into breakers on only the same phase. Was a weird to troubleshoot until I realized all fixtures were on a phase which also had a hideous noise maker on that phase.
Don't know how much X10 you have. But in todays world of, cheap wall plug adaptors which are practically all switching supplies whose potential to reek havoc on X10 power line codes is high, I would consider getting a repeater (also called "amplifying coupler"). The best is the XTBIIR from JVDE, which can be found on the same link that Brian H included in his comment yesterday. The one that X10 sells isn't bad, but does not have the power of the XTBIIR, hence has a harder time overcoming noise.