I believe it's because BIS 2.6 allows the BB to move emails directly to Trash. It no longer goes through the IMAP/Trash folder. For that reason, it doesn't matter what settings you apply through the gmail labs Imap settings. Same for Imap/Sent folders.
Have you tried setting up your email the old way? ie. recreate your gmail account on BIS but don't type your password & enter the server info manually. This advice worked for some people who had lost their gmail filter functionality under the 2.6 setup. Adding the account the old way solved their problems.