Using version 9.0.0.269

When I use a Logistical sorter to sort by ModID, it only sorts blocks, not items.
It also does not sort non-solid things like pipes.

as you notice, mekanism is based on 3 parts, mek tools, mek gen and mek in general
if you set it right, then you will have no problems

Thats not the issue.
For example, if I set the filter to "Mekanism", it does not filter Logistical sorters or Enriched alloys.

I'm afraid that the real fix for this is not going to come until the 1.9.4 release, there are some strange issues with the way mod ID filters are handled.