Minecraft version: 1.10.2
Forge version: 12.18.2.2133
JEI version: 1.10.2 - 3.13.3.377
NEI version: 1.10.2 - 2.1.2.163

So the torch renders fine, since that slot isn't being affected / rendered over.
Slots that don't have a stack-size indicator also render (somewhat) fine, as seen on e.g. my TConstruct tools in the hotbar.
Though, even those seem like they are a bit too bright for the the gray overlay applied by the search filter.

Please verify the issue with the latest builds from CB's site.

Exists in 1.11, Though i fixed this..

K, 100% fixed in 1.11 http://ss.covers1624.net/qyddh8a.png