Please be aware that an antenna is designed for one or more frequency ranges, not system types. The 800 MHz antenna is designed to provide best receiption on the 800 MHz band of frequencies (analog, digital, trunking, conventional, clicks to turn on and off sprinkler systems, whatever). The standard duck shipped with the scanner is generally a VHF-Hi antenna (that often has good results on UHF as well) so it works better on those bands (but not necessarily so well on VHF-Low or the 800 MHz bands).
From the performance issues you're talking about I suspect that the "Digital Trunked Systems" are all on the 800 MHz bands and the "Conventional Systems" are on the VHF-Hi and/or UHF bands. This is why you're getting the performance you see. If your area had one of the VHF-Hi Digital Trunked Systems, the 800 MHz antenna wouldn't pick that up nearly as well as a Conventional System that was on 800 MHz, but the stock ducky would.
Please be aware that antenna makers do not want to say that an antenna will not work somewhere. When they say it will work "on all bands" but lable it for just one or two (such as "800 MHz" or "VHF/UHF") you should really only count it working on the specific bands and for "all other bands" think if you get a signal OK, but there's no promises that you will.
I have several of the "800 MHz" antennas from Radio Shack and they are very good for the 800 MHz bands. They do not work very well on the other bands though. I can get VHF and UHF signals with it, but only from closer/stronger stations than if those stations were on the 800 MHz band. I also have several dual band VHF-Hi/UHF antennas. They pick up stations on the VHF-Hi and UHF bands great, but don't work as well on the 800 MHz band stations.
It's not that either antenna is bad, it's just that you're asking them to do something they really weren't designed for. In the past, I've carried heavy loads of supplies in a station wagon, a standard car, and a truck. While they all worked, using the truck worked best. I've also had several folks (about 10 or so in each) ride in a van and a 2 seat sports car. While those in the sports car had fun, they weren't very comfortable and were glad to get out after the 3/4 mile trip (and the campus police officer just gave us a warning). Those in the van were comfortable for the several hundred mile trip.
Although the station wagon and car can haul freight they didn't do it well. Although the MG Sprite could transport 10 people at once we won't do that again (or so we told the officer). The engineers that designed them wouldn't recommend it either, but the folks that market the stuff would probably list them as features (although the legal team may remove some, such as the 10 folks in the MG Sprite). That's why some antennas designed for a single band or even as a dual band coverage will indicate that they'll also work for every other scanner band, and not mention that although it may work, it probably won't work very well on those it wasn't designed to handle.