Import photos / Synchronise folder issues 3.5 RC

Question

Having spent a couple of weeks restructuring my image schema I tried to update LR 3.5 RC to the new directory structure.  This involved lots of UPDATE FOLDER LOCATION, IMPORT PHOTOS and SYNCHRONISE FOLDERS across about 1500 folders and about 500,000 image files both NEF and JPG .
There are several problems I've come across.  The main one is the number of files listed by LR as contained in the folder do not match the directory contents. Scynchronise folder doesn't remedy the problem although the numbers found in the first part of the process, counting files seems to correctly identify the numbers involved.
I have a directory which the OS reports as containing 353 files (all JPG) LR reports 290. Synchronise folders dialog counts 71 in the import new photos dialog box.
Clicking SYNCHRONISE brings up the import screen. With the "Don't import suspected duplicates" ticked, the lower left corner of the screen tells me; 68 photos selected, ignoring 8 suspected duplicates (there are no duplicates!) 277 previously imported files.  None of those numbers seem to line up...
Clicking import puts 5 images on screen as being imported and when control is returned 3mins 45 seconds later, LR notes the directory containing 295 images. (still not the expected 353)
I then remove the folder from LR and add the same folder from the File menu using IMPORT PHOTOS. Now I'm shown (bottom left corner again, 345 files. (check all, don't import suspected duplicates.) 2mins 30sec later and LR reports 345 files.  Syncronise folder counts 8 files but the import screen is now blank. This doesn't happen every time but on 9 folders that I counted, it happened 5 times.
On another folder, where LR reports only 1 file (OS correctly shows 64 files) 63 files are incorrectly identified as being duplicates!
Where a folder has been moved and LR shows the folder name with a question mark; "find missing folder" (which BTW defaults to the catalog location...so to just point the lost folder up a level to the parent folder, 5 clicks and some mouse scrolling are required every time! A pain when you have to do it 1500 times!)
but back to the problem, having found the right place to point it, merge is an option where the folder name is already found. again on an intermittent basis, the error wording was something like (attempting to close with 1 process still active(?)  You can click past the error and all seems to work ok,  but I wonder if it is connected to the error above?
Is anyone else finding this issue or have any suggestions how to work around it?
Any suggestions gratefully received!! :-)
OS is XP, 4 gig memory, quad core with twin 1 gig graphics and twin screens.

Answer 1

further to the previous...
Just tried the REMOVE and IMPORT PHOTOS trick on a directory that had incorrect numbers in it and noticed that of the 295 files that the OS sees, LR insists that only 268 exist and 26 are duplicates!
26 duplicates in a directory that LR knows nothing of?????? Unchecking Don't import suspected duplicates brings the total to 295.
Hmm, bugs in the IMPORT PHOTOS and / or  DUPLICATE finder sections with 3.5! Doesn't do the same thing with 3.3, (checking 3.4)