Hello,
What version of Flotr do you use ? we had the same problem, a long
time ago, but it has been fixed in the latest trunk (http://
code.google.com/p/flotr/source/browse/#svn/trunk/flotr/flotr/
prototype).
Tell me if you still have the color problem with this version.
And for the displayed values, I don't know what to do, we should maybe
add another feature to find the best place for every label, but this
is not on my TODO list yet.