We have used Lytec for 15 years and I know exactly what you are referring to. When we first purchased it, it was a reasonably priced PM system with great functionality. However, once they got bought out (NDC) the prices went up. They used to target the smaller to middle sized offices. Now it is priced for more for middle only. ALso, the upgrades are costly and disruptive. We actually had purchased a separate program that worked with Lytec for our electronics. We didn't have any clearing house fees, but that program was an extra $1500-$2k per yr for updates and support as well. For us, worked out because it allowed us to submit claims electronically, direct, without a middle man. HOWEVER (and getting to my point!) we found it necessary to consider other options. The web based softwares seem to offer more than the server based ones. We researched several, but for us, the cost was, well frankly, it was outrageous. One actually wanted $20k for setup and $17k per month. After much research we found Xena-health which is a web based software that has a very reasonable monthly fee ($99-$149 depending on if you are a provider or a billing service) but has all the functionality (plus more) of the other web based softwares. They are able to offer the software for a much more reasonable price because they are using a new technology, SAAS. We are in the middle of our conversion and have been using them for about 6+ months. We are transferring slowly due to the number of providers we bill for. If you would like a demo, I can arrange one for you. (They are working on having a demo on their web site, but it's not available yet.
Best of luck!
Michele