I've repaired several Access 2007 database with not one problem like you're mentioning.
Were the tables you deleted empty?
Also, that would make me wonder whether Access is automatically resizing itself upon deletion of said tables. Perhaps you can try deleting some large tables in a database (of course, use a fake database or either a copy of an existing database), and check the file size before/after each deletion to see if it's changing.
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"If to err is human, then I must be some kind of human!" -Me