Do not know what a CIR is???? I do not use such an acronym.
If you are using win total there is a standard list of functions at the top(Athena Version) with a "Sign" function. It will only work if you have set up a digital signature with a pass word. Yo can call tech support and they can help you set it up if you have not done so already.
Compliance Inspection Report... Make sure you have the major form selected for the "CIR". Clone your original 1004, swap the major report forms out on the cloned report, change the invoice #/order # and amount you charged so you have a new assignment on file, add your photo pages, complete the CIR, sign it, then send the new .pdf pages that correspond with the CIR. Shouldn't be much more difficult then that.
The way I am reading your problem is the form is in the report, but the signature is not showing. If this is the case it is the settings of your signature. I had this same problem when I first installed WinTotal. My signature would show everywhere in the report, but the CIR. Call support and they can give you the correct settings in no time, or you can try to play with them yourself. Good luck.