I just spent a good bit of time today on the phone with this problem. No solution yet.
I tried re-installing the X2 version of SD3, no go. Did a full re-install of X3, no difference. Did the ctrl-shift/double click/ok bit, no difference. Did advanced install of just SD3 from the X3 install, no difference.
I too have also lost SD3 in X2.
It exists as it should in the correct folder, containing the dll file. It is properly referenced in the plug in paths. It worked before in X2, then disappeared from X2 and never showed up in X3 after the X3 install.
It's starting to look to me like all signs are pointing to a conflict with the X3 install, not a conflict with my registries or path assignments.
I'm at a bit of an end for creative approaches to this. Anyone have any ideas?
-Thanks.
#####EDIT DEC 5, 2013#####
I realized that Session Drummer 3 was coming up listed in my plugin manager as Session Drummer (no identifier for which version)! I saw it and Session Drummer 2, but no Session Drummer 3. Well, I got curious, opened Session Drummmer and found out it's really Session Drummer 3 (face to hand - d'oh!). I don't know if this threw anyone else off, but hopefully that helps.