It's well known that the text editor, used in Moodle up to 1.9.9, HTMLarea has numerous problems. In Moodle 2 there will be a different editor: TinyMce.
Workarounds in the meanwhile :
- If you need the users to interact with the table, in a wiki for example, you can try creating the tables in an external text editor (KompoZer, Dreamweaver...) and importing the code.
- If you just want the users to look at the information, you can create the tables in Word, Excel, etc., take a screenshot of them and import them as images into your Moodle web pages. They will be perfectly integrated and not appear as popups.