First I want to say thank you for sharing your custom sidebars plugin - Thank you!
I have one problem that took me awhile before I understood what was causing it. I have a website I am testing that is a classifieds site using custom post types.
For all main categories I have created a custom sidebar and have also checked the subcategories to use this sidebar as well. The Problem: When there is one ad in a subcategory, the master category count=2 and the subcategory the ad is in =2 while all other subcategories show an ad count =1, but there are no ads in them.
This problem is not specific to sidebars, but also in main content window (I'll explain):
Parent categories on left side (+1 to count is added even if there are no ads)
When parent category (even subcategory) is click on the left then count is correct on left, but the sidebar displaying additional subcategories is not (+1 to count is added even if there are no ads).
I hope you understand and can help with correcting this issue.
EDIT---> The sidebars work great! It's just the counts are off whenever I implement them. Also what I found interesting is if I disabled the plugin the category counts were still incorrect. In order to correct, I had to reactivate it then edit each sidebar and uncheck where it was to be displayed (ie main category & sub cats).