We use BamHI from Invitrogen, routinely digest for just an hour in 30 - 50 ul volumes at 37C, and always gel purify our digested vector and insert segments through an agarose gel with guanidine HCL added as UV protectant before ligating, but these don't seem to be related to the problems you're having...
I just got interested in this part. Do you have any protocol for the guanidine HCL loading and it's function as UV protective?
Because by chance I'm doing a restriction digest for cloning tommorow (and yes, with BamHI as a matter of fact) and since I do not clone much I'm looking for any tips how to increase efficiency.
My colleague had serious problems with cloning after gel extractions, until he started using a different UV, that has separate UV-A,B,C UV tubes. When he started using UV-A or B only for cutting out of gel, the cloning started to work.
BTW, as I say I didn't do much of a cloning, and I routinely digest in 20 ul reaction volume (all are NEB enzymes). I have never had any problem with BamHI cuts, but I have with other enzymes, and in several cases increasing the reaction volume to 50 ul or decrasing the volume of DNA added, improved the restriction greatly. Some of RE are specificaly sensitive to salt concentration changes, as it seem. We have several incubators set on 37, on longer restrictions I put the tubes in there, as there is no temperature difference between the bottom of the tube and the top, it decreases water precipitation on the tube lid and keeps the volume stable.
Also in cloning, my boss swears on phenol:chlorophorm purification of all fragments, to get rid of nucleases. He thinks they are the worst enemy for the fragile overhangs. But on the other hand, in his days, cloning was set up on a bench and not in the hood (where all the sensitive reagents and ultrapure water is now only oppened).