Received your file (attached) and went through it. Your proxy config seems to be the issue. If you say it works fine then after a while it stops it seems to be a case of resource exhaustion. For those familiar with squid your cache will die on you silently if you run out of HDD space - I think there's a similar case here. Either its memory running out or available connections.

What are the specs of the PC running the proxy? Be sure to check the free RAM & HDD space under /system resource print

Try these options:
As for your proxy access rules...umenyonga watu kabisa. :)

Have you read this? http://wiki.mikrotik.com/wiki/How_to_make_transparent_web_proxy

Finally, perusing the mikrotik forums always helps as you almost always find someone asking a similar question: http://forum.mikrotik.com