It's not really a FSO problem. The same basic code has been in use for 5 years, but the problem only showed up about 2 years ago, without the code on our side ever changing. Although we could get around it, doing so would add to code complexity and compatibility issues (ie, we have to do it manually, something that SDL handles for us at the moment). Fixing it on our side makes the code less portable/compatible, in other words.
Basically, there is no ETA for getting this fixed from our side, and it certainly won't be happening for 3.6.10 since you can get around it simply by using v-sync.