Have you voided an invoice? Sure you have not done a sales order?
At some point, depending on what you have done they will not match, the reference number is different to the system number.
The reference number is your unique number/ value for each transaction: But the system needs a unique number too -
read here and
also read this topic.
So in all the inquiries, use the 'Reference' column to find the right transaction, from there you can see the sys# or order# related to your reference number and then for further investigation if required. (so for the moment ignore sys#, order# look for your unique reference number)
Yes using a "Direct Invoice" does create 'background' transactions
Have a good read about:-
Simple Sales Process
Intermediate Sales Process
Complex Sales Process
here and the related linked pages
You can 'reset' the reference number in Setup->Transaction References, but at some point they will go out of synch again so not advised.
Best advice for a FA beginner is to setup a training company, try things out on there; along with a good read of wiki and this forum, using the training company you can make as many mistakes as you like.
If you are doing something you are not quite sure about on your actual accounts, always make a backup 1st.
There's also some links to learn the basics of accountancy in the wiki as well
The FrontAccounting Wiki(Manual, examples, tips, setup info, links to accounting sites, etc) https://frontaccounting.com/fawiki/