You won't have a problem going back to Python 2.x after learning Python 3, or vice versa. There aren't too many differences. (Some standard library changes, print is a function, all strings are unicode -- you'll never notice most of them).
Realistically, if you learn Python 3 now, and get a job working with Python, you will almost definitely be working with Python 2.x for right now. Python 3 hasn't gained wide adoption yet. However, Python 3 will be more adopted in the near future, as a number of libraries are being ported to Python 3.
If you need to use Matplotlib specifically, then you should use Python 2.7 (no sense in using Python 3 right now if the library you need doesn't work for it). But learning Python 3 first will by no means put you at any disadvantage and may put you ahead of the curve when most people finally make the switch.
There's also nothing stopping you from using both (Python 3 for learning/experimenting, Python 2.7 for work).