I just upgraded to X3 from X1, and boy was I upset to discover that none of my templates opened, and very few of my projects opened! Same exact symptoms you described at the start of this thread. Thankfully, it didn't take me long to narrow down the problem was related directly to the Philharmonic VST. It was a serious relief, because it was starting to look like X3 wasn't going to work for me AT ALL.
I opened up a project in X1 to remove the references to Philharmonic and saved without, and then X3 opened the project without a problem. That's when I discovered my Philharmonic.dll wasn't even in the 32-bit VST folder (because I'm on a new computer), so I figured the problem was because it was MISSING. Moved the .dll over and tried opening the original project in X3... still no luck. I only found this thread after I figured out the problem, so it's nice to have the diagnosis validated. I tried your work-around, and that didn't work either.
Further symptoms of this issue: during the period when Sonar X3 SHOULD have opened the project but the loading activity icon just spins, it starts causing erratic behavior of my PreSonus fader port control surface: lights start blinking and the motorized fader sputters.
For now, it appears that if I want to use my Philharmonic, I'll just have to stay inside X1. Not that big of deal, and certainly NOT a deal-breaker for using X3. I can live without it going forward, now that I have many other orchestra sample libraries to cover that gap.
Mostly glad to discover I'm not the only person with the issue, and to know I can continue to use X3 for all my future projects. It just means I'll have to clean the Philharmonic out of all my templates.