Koumajou Densetsu behaves quite strangely in Hourglass. The game itself runs at 60 FPS, but the input is delayed. Plus, the BGM plays in slow-motion. The resulting input file is only ~50 frames long for ~40 seconds of gameplay (I should note that I set the FPS in the Hourglass window to 60).
Hourglass log
Secondly, Touhou Seirensen ~ Undefined Fantastic Object has some issues with the BGM in Hourglass (it only plays the first few seconds of a song indefinitely). Plus, the game claims to run at 75 FPS in-game, which is 25% faster than usual (the game normally runs at 60 FPS) (again, I set the FPS in the Hourglass window to 60).
Hourglass log
Note: Both games are updated to their respective latest versions. I used Hourglass r81 with default settings. I should note that the games run just fine outside of Hourglass. I'm using Windows 7 Home Premium x64.