Y axis skips

I'm having issues with my y axis skipping steps. It runs fine and will suddenly have a fast movement that causes it to skip. I'm not running super fast speeds- my feed rate and travel are at 50. I've slowed the feed rate down as much as 40% with the manual control and get the same results.
Besides the obvious setting the feed rate to a much lower number is there a setting of some sort to slow down the jerking or acceleration? I've seen the jerk setting but am not sure if that's the setting I need to try.
I do have a larger print bed- 11.5" x 11.5" x .125 aluminum. With the heat bed and glass it is probably on the heavy side but I recently switched from bronze bushings to makerslide to try to fix the problem. And as a final note I tried adding a 2nd stepper motor to the Y axis today with no luck.
Thanks

Reducing jerk and acceleration in the firmware may solve your problem. Skeinforge has no control over that.

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That'd what i thought. Put. the heat bed on a diet last night and its working better but still have to remove some mass. I would think the problem would be prevalent throughout the print but it seems more so during the first layers.
Thanks for the reply.