Hi,
Main reason for this is that you have defined that pool will have only 2 digit numbering and next number 100 requires 3 digits. If I remember correctly view will use the next number of highest used currently, so it should start from the 01 if you empty the pool by deleting all desktops from the pool. If this is not the case I would check if there is some kind of inconsistency with view's connection server's ADAM database, view composers database and the linked clone VM's actually in the Vcenter's inventory.
another kb gives instructions for manually deleting linked clone vm, but I would first check if there are extra vm's in the ADAM and if there is I would create a support ticket before starting to remove them to fix the original problem first which has caused this to happened.