First, see if that file is there.
Did you change either of these elements in the project config file?
/* path to MyComponent source files */
'mycomponentRoot' => $this->modx->getOption('mc.root', null,
MODX_CORE_PATH . 'components/mycomponent/'),
/* path to new project root */
'targetRoot' => MODX_ASSETS_PATH . 'mycomponents/' . $packageNameLower . '/',
If I'm understanding you, you can create a new transport.zip file with either PackMan or MyComponent, but that file causes trouble in Package Manager.
I can't think of anything that would corrupt the package that would affect both MyComponent and PackMan builds, other than some issue with the version name or number (like a space or other illegal character in either one).
A PHP syntax error in one of your files could possibly be causing the trouble. A missing quote in the lexicon file, for example, or something similar.
It's also possible that MyComponent and PackMan both have a problem with MODX 2.5.1. I haven't had a chance to test MC, though I think there are people on 2.5.1 who are using it successfully.
Sorry I couldn't be more help.
I'm glad you got it sorted (and that it wasn't a problem with MyComponent).