I am not aware that WMC supports more than one \Recorded TV folder to RECORD new content. I'm not even sure I know how you went about doing what you think accomplished that. Can you elaborate?
You can add multiple \Recorded TV folders (to the "Recorded TV" list in WMC settings) on other drives for playback, so that you can manually move WTV content from your primary one-and-only recording folder to these secondary "playback only" holding tank folders. This allows you to have LOTS of capacity for storage of previously recorded content, while still keeping the one-and-only primary recording folder relatively empty... if it's not really large enough to meet your ongoing regular needs without housekeeping every now and then to move to other locations.
As far as actually designating that the new recordings go into "multiple recording folders" and expecting WMC to "load balance" the recordings (i.e. spreading them evenly across the multiple folders in the pool) much as real DVR's do when an external SATA drive is attached, or when other TV/DVR products like BeyondTV do (they actually have a notion called "recording pool" of multiple folders that you can specify)... well again, I've been using WMC for a long time and I am not aware that anything but one and only one \Recorded TV folder is used for recording new content.
Again, multiple \Recorded TV folders are available for playback (you simply add as many of these other drive locations as you want, with each one automatically created by WMC as "\Recorded TV" on that drive). They will all participate in your recordings list. But there's only one folder used for new recordings... at least to the best of my knowledge.
And it's up to you to manually maintain that one-and-only recording folder if necessary, to manually move WTV files to your secondary \Recorded TV folders thus freeing up space for new ongoing recordings.