This certainly is strange. Ketamine should certainly dissolve. I don't see how it could have gotten converted to freebase. It's possible to try adding an acid of some sort to turn it into a water soluble salt if it did turn into a freebase. You just have to be very careful not to add too much acid. You want the pH of the solution to be neutral, especially for injection.
Also since you're working with powder and IM'ing you really should put it through a micron syringe filter, it could cause an abscess if you don't.
It's also possible that the stuff that's not dissolving is just impurities. Is the bulk of the powder dissolving and you just have a little bit of stuff remaining?
edit: thought I should mention that a freebase is the form of a chemicals that is not soluble in water, it can be turned into a water soluble form by adding an acid. Also I've had K in a baggie in a drawer for 3 years and had some about a couple months ago, absolutely no loss in potency, it was still nice, clear crystals.