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Application loosing focus after using Desktop (minimize all/quicklaunch) button.

Our company is running an ERP Software (Encompix) Client\Server system. We have users who access this application using Citrix. The system is working fine exept for an odd issue where when a user clicks the Quick Lauch Desktop icon to minimize all then attempts to go back to the application the screen is blank. This does not occur when running the client directly only when running the application from Citrix. I have seen several related issue posted on Citrix site, but none directly related to Desktop button. The application uses multiple windows as you drill down thru data. Server 2003 TS/Citrix Presentation 4.0. Clients running XP SP2.
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dpetr000
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Is the Citrix icon a Published Application or Desktop?

Also, I use the local "Show Desktop" all the time without hitch.  I'm curious to find out what is happening.
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coenewnes

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No the ERP application is published. We drag the icon for the application from Citrix folder to desktop. The users then access the application by simply double clicking the shortcut. I believe the issue is due to the way Citrix handles the multiple windows created by the application. If you open the app and drill down thru data this opens multiple windows. When you minimize all, all the windows minimize but when you attempt to select the child window again they show up blank. Its seems that the application looses it's child parent relationship. I was able to run SPY++ on the application using both normal, citrix connections. The class name changes for each type. Citrix sees the window or app as Transparent Windows client (class). When I run the application locally it shows as ProMainWin (class).
Thanks for the response.
Published Applications, especially the seamless windows, have a number of known issues.  Have you tried this via a Citrix Published Desktop just to see if it works correctly?

I have encountered applications that don't run as a Published App but work fine with used on a Published Desktop.  In those scenarios, we have released a desktop instead.
Yes the application runs fine from a published desktop. The interesting thing is that this started after we upgraded to 4.0. I reinstalled the old client and tested this process and I don't have the issue. I have seen several work arounds for other applications like SAP I have tried them with no success. Something must have changed in the way Citrix handles Transparent Windows Clients. I don't really want to publish desktops for all users to get 1 application to work. This does appear to be a known issue (CTX101644) but I am unable to get any of the fixes listed to work. Unfortunately I didn't setup the original Citrix Server so I don't know if anything was altered. When connected to the published desktop the ERP software shows as ProMainWin (Class) this is the same as the direct client. The Transparent Windows Class is used in both the older Citrix and the new Citrix. Do I just chalk it up to this feature no longer working? Any suggestions would be greatly appreciated!
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We run a medical app called Nextgen that is also experiencing the issue of losing focus to other apps that are also running via PS 4.0 at the same time. We do not publish the desktop. I've tried to use some of the seamless flags (CTX101644) but for the life of me i cannot figure out how to get the correct dword value changed. I wanted to try and see if item 15 listed in CTX101644 would help in our situation. Does any one know how to get that value into SeamlessFlag?
Well not exactly the solution , as noone else has attempted to chime in I quess it boils down to poor programming and hopefully this will be fixed in a future release. Thanks for the effort.