I'm constantly watching units dropping into ePick and the stats on MPM for both SFS and OPU, and I'm positive it's updating correctly. You just have to remember that it's really delayed. If it says last updated at 8am, the data it uses is from like 7:15am. The desktop page mentions the delay on a banner up top.
Go into a batch, pick an item, then back out and see how many eaches are still available to be picked. Make a note of that number and then check and see how much it's increased when you finish picking your batch. Keep doing that all day and you'll start to see how it increases about the same as MPM.
I'm 90% sure that the warning on Workbench was from the screwup on Monday, and was posted after it happened to warn everyone to watch out for late orders dropping due to that system lag.
The higher volume of orders is probably just because they didn't realize how popular the different sales would be this week (Toys and Grocery, plus Shoes and Swim).
You guys just need to pick your carts neater. I've been using the 3-tiers for this for a few years and it works fine as long as you keep it neat and use the space effectively.