MC1061/P3 minipreps...

[Bryan J. Maloney]

A few possibilities:

The Maniatis method can cause problems with "indigestible" minipreps.
This is often due to alcohol remaining in the DNA.  I try to be pretty
anal about rinsing with 70% EtOH and then drying to eliminate the 
alcohol (yes, I know that many manuals warn about the dangers of overdrying,
but it's never seemed to be a problem for me).  If you've got lots of funds
to spend, you could try a product from a company called Qiagen.  It's a 
column elution system which relies on alkaline lysis and then salt-elution.
We have pretty good success for moderate-scale preparations with the
columns we use.