Try to introduce as much variety as you can into the dynamically generated meta descriptions. I found that having at least two positions in the meta descriptions that are filled in dynamically usually does the trick. Depending on the way your page content is generated, you may be able to pull in significant bits of text dynamically from the page content, too. It's better to duplicate what's on the page exactly than to be close-to-duplicate across several pages.
If you're only talking about hundreds of products and not thousands, it might be worth the effort to make a project out of writing those tags anyway. A couple hundred really isn't all that impractical, especially considering that it can help your traffic and sales.
Quite apart from the meta descriptions, it's also very likely that if the onpage product descriptions of these "1000s of products" you mention are dupes of manufacturer's boilerplate, Google will look at your content as duplicate and not rank you.
I suggest you run some of your pages through Copyscape and see what they report. Chances are very likely that that is your issue.