I just started my website a few months ago and some of the backlinks that I had that showed up in google webmaster tool's that where there arnt there any more, but the link is still where it was. why is that?

Was the niche of the site where your link is located related to your site's niche? Because if it is not, google might consider this link a quality link.

In my experience, google webmasters tools update its back links in about 10 days.And some links do take time to appear at GWT.However,it does not mean the link is a quality link if it's on GWT.

Google's webmaster tools link system is crap.. ignore that

WMT is not a real-time tool. Different pages within the tool are updated with different frequency. They seem to be updated randomly - sometimes 7 days, 10 days, 2-3 weeks, etc. So you're likely looking at old data.

It's not uncommon for links to disappear off of a page yet it still be reflected in WMT. Same happens in Yahoo! Site Explorer.

This is frequently the result of "Recent Comments" widgets. You post a comment on a blog, and suddenly you get a link from every page on that blog due to the "Recent Comments" widget. The seach engines crawl your site while a link to your site is shown in the "Recent Comments" widget and give you credit for links from LOTS of pages on that site, not just the post page where you commented. Then 10 comments later your link rolls off the "Recent Comments" widget.

Both Yahoo explorer and Google webmaster tools are not accurate 100% . Both of them show backlinks that are indexed by their search engines and none of them show all backlinks of your website.
Yahoo explorer shows only 1,000 of your backlinks but it shows the total number of your backlinks too. And Google webmaster tools shows a bit more of your backlinks but none of them.
But note that all of your backlinks will be counted for ranking your pages and also for detemining the pagerank of your website.

not all of your actual backlinks will appear on Google rest assured there's nothing to worry

Google's Webmaster Tools gives you a snapshot of inbound links. Try using yahoo's site explorer for a more definite list.

I always check my back link from Google toolbar. Google toolbar is always right.

Google backlinks count depends upon the backlinks pages caching status. Rather look in search google, yahoo and msn search bar. That will give you a better picture.

Don't worry. google webmaster tool will update later and you will not see it.