When you say its not counting what you are collecting at your neighbor's be sure that the mission you are working on says "neighbor's homestead" , Other wise the tasks have to be completed on your own homestead. 

One solution you can try to fix your collections is to delete your flash cache. You can do this by going to the link below and clicking the button that says delete all sites, then trying to releoad your game. I have the best results when using Google Chrome over FireFox and IE.

 http://www.google.com/search?client=browser-rockmelt&channel=omnibox&gcx=c&sourceid=chrome&ie=UTF-8&q=clear+flash+cache