Sure about that man? You can look under FOMM
There should be a notice like this under the description WARNING: This plugin has the file extension .esp, but its file header marks it as an esm!
Maybe it's something else
An easier way to make FOMM show your ESM-ified ESPs is to open the "Settings" dialogue (either from within FOMM, or from the "Advanced Setup" shortcut in All Programs==> Fallout Mod Manager, if you checked the "Create shortcuts for command-line utilities" checkbox during installation) and
check the "Show ESMs in bold" checkbox.Once done, all files, no matter their extension, with the ESM flag in their header will be shown in bold text in your list. It's unfortunate that this setting is off by default, but even so, it's a scandal that so many don't even know it exists, because apparently no one ever glances at things like "Settings" to see what their application is capable of.
In any case, it saves a lot of trouble, since you can then immediately see when FO3MasterUpdate has done its work.