Hey Billy, I'm getting something similar.
If I go to TV Shows, then folders, add a new show in the r/hand column, save changes, go back to main browser.
Now, hit 'TV Show Selector', and then 'Scrape with selected options' and after the scrape is complete, MC switched over the the 'Main Browser' tab, where the newly added show, doesn't appear.
Now, this is all done without switching away from MC, not closing or re-opening, kinda a step-by-step sequence.
If you close MC and re-open, the new tv show re-appears. Also, if you hit re-build tv shows, it re-appears. If you add the new folder and close MC, it works without a glitch also.
I've just been repeating the sequence using 'The Professionals' as a new show.
PS, also it doesn't matter if you have episodes in the folder or not.
I know this is a hit/miss glitch that'll be hard to pin-point, but just thought I'd clarify what I'd found.
One other thing.
If I have Windows Explorer open behind MC, and add a new tv show folder and hit save changes, MC disappears behind other open windows and the dialogue box 'changes saved' appears. clicking OK, and MC stays behind the other windows so you either have to 'ALT-TAB' or click it's button on the task bar to bring it back forwards.
Cheers, and it's still the greatest program for TV and Movies.