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Applications running under wine literally takes several minutes (10+ mins) to start. If I check with the system monitor, that application will just keep on sitting with the status pipe_wait under Waiting Channel.

And this is not with just one application, its with everything running under wine.

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How do I go about troubleshooting this?

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This question appears to be abandoned, if you are experiencing a similar issue please ask a new question with details pertaining to your problem. If you feel this question is not abandoned, please flag the question explaining that. :) –  Ringtail Feb 26 '12 at 5:38
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2 Answers

Try winetricks

Make sure you have your universe repository enabled, then:

sudo apt-get install winetricks

Winetricks is an easy way to work around problems in Wine.

It has a menu of supported games/apps for which it can do all the workarounds automatically. It also lets you install missing DLLs or tweak various Wine settings individually.

It can be used via gui or commandline, whichever you prefer; the commandline mode is particularly useful as a building block in fancier wine frontends and in automated regression testing.

Here are a few tips on using Wine with Winetricks:

Installing - More about Wine and Winetricks and how to install them
RunningInstalledApps - How to run apps installed with Winetricks
FeaturedGames - Screencasts of installing and running a few apps with Winetricks
ResettingScreenResolution - What to do about games that don't restore the screen resolution 

And, for people not afraid of a little programming:

AddingNewVerbs - how to extend Winetricks to support your favorite apps 
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What version of Wine are you using? What specific program? Could be a dependency issue with that particular program. Have you checked the Wine App DB to see if there is anything you can do?

http://appdb.winehq.org/

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I am running the latest 1.3.16 version and this is with every app on wine, not just particular one. –  Ashfame Apr 2 '11 at 20:06
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