How are you extracting your DNA? Are you doing any kind of cell lysis (e.g. bead beating)? 

Glass beads will cause shearing of genomic DNA.

You need a protocol on High Molecular Weight DNA extraction.

I've used a modified version of the protocol in the paper below for genome sequencing of molds. I didn't use PacBio, but the gels showed very high molecular weight DNA.

The modifications I made are described in my thesis (not yet formally published) (see link).

Article DNA Extraction Protocol for Plants with High Levels of Secon...

Thesis Geomicrobiological aspects of the (bio)leaching of weathered...