Problem with ID Tracking

It sounds like there are unwanted overrides. Check for forced line breaks in your text causing extra pages and remove them using Find/Replace. For tracking, ensure no Character Style is overriding your Paragraph Style—set it to and reapply your style. Hope this helps!

@m5heath

Can you upload even a small sample INDD file? 

Will save us a lot of guessing... 

The workflow you've used often creates very bad styles, in Word, that are not worth importing or preserving on ID import. Unless you are going to do a pretty thorough cleanup in Word and assign clean, defined styles throughout, your best bet is probably to import the content as little more than body text. Either convert it all to a simple body format in Word, or, once placed in InDesign, select it all and assign a simple Body format to it all. Then build and apply your formats.

That is, don't try to sort out or fix details like this tracking issue; smack it all down to base text and start over. You will no doubt be clearing and removing other subtle, annoying faults with the styles by doing so.

There are three or four workflows with a project like this, but at some point, with all but the best source material, you have to clean the grit out of the content and assign consistent, valid styles. It can be a mistake to spend too much time trying to preserve wonky imported styles, and use ID's features (many) to format the content once you have it imported.

ETA: Said everything but this: import with stripping of all text and table styles to achieve the above and elminate an unnecessary number of style issues.