This is a known issue and currently it is unresolved. Please check this document in page 11: Release Notes - Intel Edison. This issue happens in the Arduino Expansion Board and in the Mini-Breakout Board, and only with the GPIO48. Hopefully it will be resolved in future releases.
We did indeed get it fixed, just after Release 2 was out the door. It will be in the next one.
Thanks all of you, hope it's fixed in the next release.
Is it possible to post a patch for this fix while we wait for the next firmware release?
I'll bring it up as open this week, but I think it will be low priority. We're pretty close to said release, and the work to open source most of this stuff is nearly done (so changes like this should be visible going forward).
If they're ok with it, I'll track down the patch. If not, you'll probably have to wait a very short time for the next release.