I think we should stop JQS before InstallValidate so that it does not cause FilesInUse problems. If the user cancels, we might want to restart JQS.

From an MSI log where JQS is running and the FilesInUse dialog is not displayed:
MSI (s) (4C:50) [18:51:56:078]: Note: 1: 2727 2:
Info 1603.The file C:\Program Files\Java\jre6\bin\jqs.exe is being held in use by the following process: Name: jqs, ID: 3808, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: svchost, ID: 1556, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: ccEvtMgr, ID: 1696, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: ccProxy, ID: 1740, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: ccSetMgr, ID: 1764, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: ISSVC, ID: 1776, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: SNDSrvc, ID: 1792, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: Rtvscan, ID: 1320, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: SymSPort, ID: 1496, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: explorer, ID: 2184, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: ccApp, ID: 2284, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: VPTray, ID: 2592, Window Title: (not determined yet). Close that application and retry.
Info 1603.The file C:\Program Files\Java\jre6\bin\msvcr71.dll is being held in use by the following process: Name: jqs, ID: 3808, Window Title: (not determined yet). Close that application and retry.
MSI (s) (4C:50) [18:52:07:437]: 11 application(s) had been reported to have files in use.
MSI (c) (5C:04) [18:52:07:453]: File In Use: -jqs- Window could not be found. Process ID: 3808
MSI (c) (5C:04) [18:52:07:453]: File In Use: -svchost- Window could not be found. Process ID: 1556
MSI (c) (5C:04) [18:52:07:453]: File In Use: -ccEvtMgr- Window could not be found. Process ID: 1696
MSI (c) (5C:04) [18:52:07:453]: File In Use: -ccProxy- Window could not be found. Process ID: 1740
MSI (c) (5C:04) [18:52:07:453]: File In Use: -ccSetMgr- Window could not be found. Process ID: 1764
MSI (c) (5C:04) [18:52:07:453]: File In Use: -ISSVC- Window could not be found. Process ID: 1776
MSI (c) (5C:04) [18:52:07:453]: File In Use: -SNDSrvc- Window could not be found. Process ID: 1792
MSI (c) (5C:04) [18:52:07:453]: File In Use: -Rtvscan- Window could not be found. Process ID: 1320
MSI (c) (5C:04) [18:52:07:453]: File In Use: -SymSPort- Window could not be found. Process ID: 1496
MSI (c) (5C:04) [18:52:07:453]: File In Use: -ccApp- Window could not be found. Process ID: 2284
MSI (c) (5C:04) [18:52:07:453]: File In Use: -VPTray- Window could not be found. Process ID: 2592
MSI (c) (5C:04) [18:52:07:453]: No window with title could be found for FilesInUse
MSI (s) (4C:50) [18:52:07:453]: Note: 1: 2727 2:
Action ended 18:52:07: InstallValidate. Return value 1.