Hello,
Couple of things to try:
Make sure you're on the most current version of Keynote. If not, run software update through the App Store. I believe the current version is 6.5.2. (2119)
Are you using Keynote in iCloud?
Can you change the Y axis to any other format? E.g. Currency, fractions, etc.
i hope one of these works for you, because I can't replicate the problem.