I had the same issue with WSJT-X "skipping" decode cycles. Very frustrating!! Through their forum, I found a workaround that seems to fix it. Just change the priority of WSJT-X to Realtime instead of the default Normal setting.
Right click on the taskbar and select Task Master. Select the Details tab and scroll down the list to WSJT-X.exe. Right click on it and select Select Priorty and from the selections, choose Realtime. Confirm it with the Change Priorty pop-up.
One issue is that you have to do this each time you start WSJT-X, even on a reboot. It may put a wee stress on your CPU but not a whole lot and only for a second or two, depending on your CPU. My shack laptop is old but it handles it fine.
I hope that helps.... it works for me with Windows 8.1 and a mighty 1.4GHz CPU :P
73, Tom VE3II