I have seen few reports here concerning VSTs automation and the connected issues, e.g. after projects save, load etc.
I don't know if anyone is already working on this, but I wrote a patch, which should address that problems.
Its against GIT Master branch and you can get the patch and see full description here
I tested this on Win32, Linux32 builds,
I will be glad if you could test it too or report any issues back.