I have this same exact problem on 2 of my 3 PC's. . .
WARNING: This is going to be a lengthy post.
System Specs for all 3 PCs (no overclocks, all XP64, all latest drivers, all current Windows Updates):
System 1:________________System 2:_________________System 3:
AMD Athlon64 x2 6000+_____AMD Athlon64 x2 4200+_____AMD Athlon64 x2 4200+ (s939)
nVidia nforce 590 SLI MB____nVidia nforce 4 SLI_________nVidia nforce 4 Ultra
GeForce 8800GTS__________GeForce 7950GT___________GeForce 7900GT
4G DDR2 PC800____________2G DDR2 PC800____________2G DDR PC400
Onboard Snd (RTL)_________Mystique 7.1 DD Live_______Audigy 1
Preliminaries:
I just built System 1 (Tax Time

) and was doing a complete fresh install. System 2 is my primary rig. System 3 is my wife's PC. All YASU versions are latest 1035. Systems 1 & 3 are now running DT 4.091, System 2 is DT 4.08 (downgraded from 4.091). All DT's set to have 1 Virtual drive, and on systems 1 & 2 the driver letters are set before the physical DVD/CD ROMs. YASU is set at default options and NOT set to autorun - I run it when i need it. All Alcohol installations have their virtual drives set to 0.
Before building System 1 this week, I bought and Imaged C&C 3 Kane Edition and played it on System 2. At the time, I had YASU 1.07 and DT 4.08. The image mounted, installed, and played fine on System 2 with C&C 3 versions 1.0 and 1.1. When I patched to 1.2, it detected the image - prior to this had never had a problem with YASU 1.07 at all. Logged in here (long time lurker) and grabbed DT 4.090 and YASU 1033. Game played great again. Patched to 1.3 - no problems, patched to 1.4 - no problems. Played the game until I beat all 3 sides, PC sometimes left on overnite at desktop, sometimes pc shut down overnite - never had a problem playing the game (DT 4.091 kept randomly unmounting my images, though). Built System 1 and installed everything fresh on it - latest versions of DT and YASU 1035, Alcohol 52% free (System 2 using latest Alcohol 120%, and System 3 also using latest Alcohol 52% Free). Installed my games, including HOMM V and expansion as well as C&C3. . . so far so good.
The Problem:
Heores V expansion and C&C 3 would refuse to run at all from image on System 1. Redid entire system from scratch again, and when I got to the games, tried each immediately after install and patch to find the culprit. C&C3 installed and played fine at 1.04. Got to and Installed HOMM V & expansion, patched expansion to 2.01 - BAM, Heroes V starts giving me "Conflict with Emulation Software." Tried C&C3 - now it does it too. Tried rebooting - did not help. Tried with and without YASU - neither game would work. Tried original disks - they worked fine. Uninstalled DT and reinstalled 4.091 - did not help. Tried YASU 1033 - did not help. Uninstalled Alcohol 52% - did not help. Never had a problem on System 2 with either game - and at the exact same patch revisions, too, so I decided to backtrack DT a bit. Uninstalled DT 4.091 and went back to 4.08 with YASU 1035 - worked like a champ on both games. Reinstalled Alcohol 52% again - still working. Shut down system for the night. Came back the next day, and BAM - the "Conflict with Emulation Software" message on both games again. Uninstall Alcohol 52% AGAIN - did not work. Rebooted PC, did not work. Uninstalled DT 4.08, rebooted, reinstalled 4.08 - started working again. Left PC ON overnite. Came back the next day, and the "Conflict" message is back again on both games. Uninstalled DT, rebooted, reinstalled - did not work this time. Upgraded to 4.091 again - still not working. This is where I am with system 1 right now. In the interest of curiosity, I decided to try System 2 again. . .
Mounted the image, ran YASU 1033 - "Conflict" message. NOTHING had changed on this PC since I had last played the game on it - no new Windows Updates, no patches, no new software installed, NADA! rebooted PC - no good. Upgraded to DT 4.091 from 4.090 - no good. Updated YASU - no good. Rebooted again, just 'cuz - no good. Uninstalled Alcohol 120% - no good. Uninstalled DT, rebooted, installed 4.08 - games worked. Rebooted PC - games worked. Shutdown PC for the night. Next day - BAM, my buddy the "Conflict" message was back again. Tried original DVD - worked great. Image just kept giving me the "Conflict" message. Got the image working again by uninstalling DT, rebooting, re-installing DT again. That is where I am with system 2. . .
System 3 works great. I upgraded it to YASU 1035 and DT 4.091 from YASU 1.07 and DT 4.08 before installing C&C3 on it (copied image from System 2 over network to her PC). My wife plays Heroes V frequently with no problems. Again all software is latest patch level. WE ARE EVEN USING THE SAME NFORCE AND GEFORCE DRIVERS (Systems 2 & 3)! C&C3 and Heroes V run on her machine without a hitch, every time. Rebooted, shutdown, left on - doesn't matter. All I have to do is run YASU and it just works - and she still has her Alcohol 52% installed. Mind you, this is the same image all the way 'round.
Sorry for the lengthy message, but after lurking on the board the last few days and seeing people being dismissed out-of-hand for this same problem, I felt compelled to make a detailed account of my own adventures in being able to keep my COLLECTOR'S EDITION GAME DISK IN MY CLOSET. There is something fishy going on with this, and I hope by this post we can find a common denominator jacking this up and get a good workaround or fix on it. If you need any other info from me that might help, I will check this thread every few hours. Thanks.