J_McLeod, I too shared your frustration at first with my Pro 1000 but the following really resolved my primer feed issues.
In a rush to reload, how many of us just fill the primer tray and start the reloading session? I am guilty of that but soon learned a quick minute spent on checking the proper primer feed attachment function will save a lot of frustration during the reloading session.
After cleaning/lubing my Pro 1000, checking shell plate timing and weighing my powder charges until they are consistent (to allow settling of powder in the hopper); before starting a reloading session, I do a QC check of primer feed attachment.
I fill the primer feed ramp with primers and without any case in the shell plate, actuate the case sensor with my finger to see if the column of primers drop freely in the feed ramp and push a primer into station #2. If not, first check to see if the primer push rod is dropping with a "click" to allow a primer to slide down - Lee Precision has a nice video on this (if there's too much powder inside the primer rod tube, you'll need to disassemble the shell plate carrier to clean) -
http://www.youtube.com/watch?v=fOhDMhYY9ug&feature=mfu_in_order&list=UL
Then I look for obstruction that's keeping the primers from sliding freely and/or remove the primers and clean/polish the slide surface as necessary (some reloaders posted they use car polish/wax to make the surface slick but I just clean them with a Q-tip). If your primers are not sliding freely even after cleaning, you want to inspect the surface of the primer feed attachment for any gouging of plastic that maybe keeping the primers from sliding freely and smooth out the surface as needed. If the primer feed attachment is too far damaged, you may need to replace with a new one.
Note that if you are using a powder that's sized smaller than the flash hole, you'll get powder leakage when a primer is not seated in the primer pocket and the case is allowed to charge with powder.
During my reloading session, since the Pro 1000 primer feed attachment is gravity based that may not fully insert a primer into station #2 base if there is any obstruction in the feed channel (maybe few flakes of powder that may leak from operation of Auto Disk), I watch the column of primers in the feed channel as the shell plate clicks into station #2. If I don't see the primers dropping to insert the next primer, I will check and/or use a small precision screwdriver/bent paper clip to help push the next primer fully into station #2 as partially inserted primer will bind and may cause flipped/sideways primer when the primer push rod comes up on the upstroke of the ram lever. If I see any obstruction/debris, I will use compressed/can air or small brush to keep the area clean.
When I refill the primer tray with more primers, I will also reinspect the base of the primer feed attachment for obstruction and clean as necessary.