These key mappings cause problems even in a default config, and I don't think they're useful. They'll be even worse for folks who have remapped keys.
If you'd like to keep the remappings, let's figure out a way to make them optional, and to get them right for the default case (by mapping 'd' instead of 'dd' in visual mode, for starters).
remove remappings of dd, dw, u, and <c-R>
The two-letter mappings cause problems in visual modes where 'd' is a
In general, I don't think that the mappings are useful, since
RunPyflakes gets run all the time anyway via various autocmds.
Just for the record, I came across this issue when searching for a way to solve the fact that I can't delete a line with d in visual select any more. One solution could be to change the "noremap" in lines 163 and 164 to "nnoremap", so they only take affect in normal mode (and not in visual mode). This solves the visual mode problems djmitche mentions.