i as well use DHP PT and never have had the issue you mentioned earlier after partials.
i would recommend that you make sure all the connections are secure on the box and port (i do not use the usb adapter, i have an older "good" laptop w/ a serial), use a battery charger/jump pack and plug in your laptop during the write if possible. make sure you are using the same modified file from the last full flash.
while i dont always use a jump pack and plug in my laptop, i try to.
since i do not know how the partial flash works entirely, i do not know if it references the change log of the file you are working on to know what to flash and not what to flash. so i try to stick to the same file and do not swap back and forth from one branch to the other...
example....
...............top swap bin option 1
stock bin<
...............top swap bin option 2
dont full flash option 1, then partial option 2.
i would only partial option 1a, 1b, 1c, etc. if i wanted to try option 2, i would full flash, then partical option 2a, 2b, 2c, etc.
make sense?
are you using tiny tuner at all? i have heard that some tables are not mapped 100% correctly. i try to limit my changes to the PT software, and only going into tiny tuner to modify a table i dont have access to in the PT.