In version 1.1.95 the auto compressor does not accept the dust as input, neither manually or with some pipes.

Find out on FTB Infinity Expert Skyblock 1.0.4.

Yeah, it didn't make it into the latest Infinity hotfix sadly. Updating Ex Compressum manually will fix the issue.

Try updating manually to the 1.1.99 release from the FTB launcher and try to reproduce. (http://minecraft.curseforge.com/projects/ex-compressum/files/2291625)
Should be working in the new version according to the changelog.
"Fixed some blocks not being accepted by the Auto Compressor even though they're compressable (including Ex Nihilo Dust)"