I know this is an older thread, but I thought I'd chime in. I've an old 2009 MBP with a core2duo and 4gbram. I modded it to hold 2 hard drives, both 1tb. One is formatted as exfat for file-size compatibility of audio and video file movement (16tb max). I also have externals with ntfs, exfat, fat16, fat32, macos hybrid. I've had the trash problem as well, and have traced one or two occurrences to launch agents, but most are "Dumb" boxes. Usually, for me, this problem is a result of the cacheing modes of disk operation having problems or locking up. What that means is that the basic deletion operation is cached until the disk is idle, but the system hasn't noted that the last operation or a previous operation is finished, so the cacheing just builds up in the stack. When you run verification on non-mac formats through disk utility, it may not be able to run because it doesn't have access to those advanced functions (it only supports a few non mac formats natively for repairs), or it cannot unmount the drive properly because of the cacheing. When you force a shutdown, you drop the cacheing problem, however, there are files listed for deletion, and others listed for read\write ops, and the journaling (file table, MBR, Partition table) is corrupted, which will cause the cacheing to fail again. IF you are on a non-mac format disk, don't repair with disk utility. Don't verify the disk there either. After a restart (safe mode not needed), run the terminal disk repair operation. If you run it in verify mode for exfat, or NTFS with MBR for the partition mode, it should automatically repair them (it runs the operation like a full checkdisk in windows, rather than a verification). Once the journaling is repaired, it might even delete the files you tried to wipe before, but that only seems to happen if the last active operation in the cacheing was in fact a trash wipe. Once it's repaired, you should be able to empty the trash again.
I use IceClean to Force Empty Trashes, then allow Empty Trashes, then I run the terminal command on ExFat\NTFS drives--especially ones connected by firewire.
I've found firewire support waning in the later mac OS (10.7 and above), probably due to the push for Thunderbolt. Firewire doesn't like cached ops, and really doesn't do well with it in erasing files. I've used IceClean to fix it, and used a full re-partition as the fastest erasing ops, mainly because the info isn't sensitive, and I need the space back. With sensitive information, stick to ESATA drives, and make sure you have either expresscard 2.0 or thunderbolt esata adapters. They function with cacheing natively, and rarely have the trash problem. When they do, just force eject, repair, and try again. If it continues to have a problem, use a utility like IceClean (check macupdate.com), and use the force empty trashes, which will bypass any cacheing; then use the empty trashes allow, which will restart your finder, and show the trash emptied; finally, verify your disks with terminal. You could do this with an automator action that does a drag and drop, or shows you the disk list, letting you copy the diskNsN information, and paste it into a text box that applies the rest of the command and shows you the result.