Hi brucerez,
To get straight to the point: I don't believe in working with OTS and Registrations at the same time (in the same song). Just switch off OTS LINK and work exclusively with Registrations.
The reason for the problem you describe might be the following: When OTS LINK is active, your (direct) pressing of a Main Variation button activates the corresponding OTS (Main A > OTS 1, etc.). In your case, however, the relevant Main Variation was already activated
beforehand (and thus initially also the "correct" OTS). Then a specific Intro was activated (which doesn't change the current OTS). But now you change the keyboard voices by loading a Registration. These voices are retained even if the keyboard switches automatically back to Main A after playing the Intro. To bring up the previous OTS again, you would have to press the Main A button again.
As I said, I would switch off OTS LINK and only work with registrations. Memorize the desired Main variation with the desired activated Intro, possibly Sync Start, and the Piano sound on Reg button #1. On Reg button #2 memorize the same Main Variation, possibly with activated Fill-in, without Sync Start, and with the Strings sound. If you then need the Strings sound after playing the Intro, just switch to Reg button #2 (manually or, if the Registration Sequence function is activated, via a foot switch), and everything is fine.
Best regards,
Chris