There are a few issues here.
1. You can use any software you like to submit but data MUST be validity error free and in the proper FFIEC format. In addition, the submission by email MUST be encrypted using only the FFIEC supplied encryption prgram (which is separate from the data entry software).
As far as everyone using FFIEC software, actually over 3/4ths of the records submitted to the FFIEC accounting for about 1/2 of all financial institutions are submitted using either Pci's CRAWiz or QuestSoft's HMDA RELIEF. (In the interest of full disclosure, I am president of QuestSoft and according to the 2007 FFIEC HMDA LAR, we had 1,554 customers successfully submit 3.78 million records). The reasons for using FFIEC software is that it is free and the government's official software. For the 4,000 institutions that submit 100 records or less, it is usually a good choice. But it also is very mannual. The reasons for using another product are that they usually automate a lot of the process (for example, our customers say they usually save about 90% of the time to scrub, geocode and submit the data). Another reason you might select a third party is customer support which tends to be live voices (vs email) and very responsive.
2. re Jack Henry. Jack Henry is one of the major core processing systems. Every system that processes mortgages stores HMDA information because it is on the loan application. However, that data is not scrubbed for accuracy, geocoding, or errors (proper combo of race/sex, etc) and that is where people get into trouble and the FFIEC/FRB gets upset. You cannot take that file export and just email it to hmdasub@frb.gov without putting it through HMDA specific software first. It is guaranteed to come back and you will have probably experience the wrath of the FRB if you attempt a second shot. This is why you usually see post on BOL refering to HMDA in a different word than Heaven and being very specific in emphasing accuracy.
All loan software products have some way to export the data out (some might charge for that) to the HMDA.DAT format. If you want to go the FFIEC software route, I would check with your Jack Henry customer support to find out how to perform that export. It should be a pretty common question during this time of year.