first to assume being a wubi dont make a difference , I ran wubi 11.10 for several months updated to 12.04 beta and ran that as well..
first thing you should know about your wubi install , some of its quirks and problems are related to windows since wubi is a window program and even though it appears ubuntu boots before windows windows boots and is running in the background
what I discovered with wubi is when your nor booting windows updates are falling behind for virus scan windows updates and anything else scheduled to run like defrag ..
I installed my wubi and never checked or booted back in to window for nearly 6 weeks the wubi install got slower and slower including boot up other minor issues started popping up ..
I booted windows windows took 3 or 4 mins to boot and the HD ran on and on as everything fought to update and install at the same time once I got things clamed on my win7 install I did a disk clean up and I checked and discovered the windows volume was 57% fragmented I ran defrag several times I even rand a dskchk for good measure and it actually found several bad sectors..
once I was done took me a whole day to recover the unused window OS , I rebooted back to my ubuntu wubi instal and it flew like a jet again and cleared up most of the issues I was having ..
your milage may vary but if you are using Ubuntu wubi install not booting to windows much or keeping it maintained it will bite you bad running wubi ..
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