I have encountered the problem more than once, and it is a bit annoying to say the least. Basically, when you build a path/arrow in Inkscape, it starts as a black curve by default. You can edit it to put a marker in either or both ends (Click on the curve, then Object->Fill and Stroke->Stroke Style), to make an arrow, for example.
Now, the problem is that if you change the color of the body of the arrow, the head will remain black, as documented, for example, in A Guide to Inkscape, by Tavmjong Bah. Not nice, uh? The solution is given in the same site, and consists on using a plugin. To do so, select: Effects->Modify Path->Color Markers to Match Stroke.
If you are a Debian user, you might encounter a problem: a window pops up saying The inkex.py module requires PyXML. This has been reported as a bug, and also happens for Ubuntu. The solution is to install the python-xml package, which is not always installed by default when you install Inkscape, it is just "suggested". This means that when you install Inkscape (aptitude install inkscape), aptitude will tell you something like "The package python-xml is recommended, but it is not going to be installed", and will go on happily. If (like me) you ignore the suggestion, you will not have the python-xml package installed, and some extensions, like the above, will not work (however this allows the users that do not want to use the plugins to have a lighter instalation, if they so wish).