Sorry in advance, I'm not sure what the proper room for posting this would be.
I spent the last couple hours, frustrated, installing new 1.4 mods, only to have all mods removed the moment I used the MCPatcher (to do the texture fix for my Steampunk texture pack).
I'm not a minecraft mod programmer, so I don't know what the cause of the problem is, but I finally figured out a solution:
1. Install new 1.4 mods as per instructions (I just installed Single Player Commands, AudioMod, Modloader w/Grass Fix, CJB's Minimap, and Humans 1.8)
2. Test Minecraft and make sure all your mods are working with the Default texture pack. You can switch to your favorite texturepack at this point, but you'll find that the lava, pumpkins and glowstone have jacked up textures.
3. To fix them, download the new BETA version of MCPatcher
4. Run MCPatcher (DON'T ACTUALLY DO THE PATCH YET) and you'll notice that it's using "minecraft-1.4.jar" as the source and "minecraft.jar" as the destination.
5. Go to your Minecraft/bin folder
6. BACKUP your modded minecraft.jar file, TWICE (two dupes, one for actual backup, the other we'll be using in a second)
7. DELETE your minecraft-1.4.jar file
8. RENAME one of the dupe copies of the modded minecraft.jar to minecraft-1.4.jar
9. Run MCPatcher (you can do the texture patch now). Don't browse to any files, just click patch.
You should be working with all mods and correct textures now.
P.S. I realize that steps 7&8 should be unnecessary (you could simply click Browse in MCPatcher and select the duplicated minecraft.jar file). However, this isn't how I did it, so I wanted to document the steps as I took them.
Again, hope this helps anyone trying to get their new 1.4 up and running with favorite textures/mods... and sorry if it's not posted in the best spot. Moderators feel free to move it if you feel it should go somewhere else.