You aren't seeing all your funds because the data for some funds is not in the data file connected to the merge document you are running.
When you are using the statement style option (set up in the Fund 2 tab in the Fund module), FIMS will split the exported fund data into separate files based on their statement style value. Thus, if you have an End and PT style for Endowed and Pass-Thru funds, then you might get 3 data files:
fndstat.txt for funds with no code
fndstat_end.txt for funds with an "end" style
fndstat_pt.txt for funds with a "pt" style
The data is split into separate files based on this style code so that different fund statement merge documents can point to different groups of funds. For example, an endowed statement might have investment earnings detailed by realized and unrealized gains, interest, dividends and fees and will be connected to the fndstat_end.txt file. Thus only those funds with the "end" style will be in that data file and thus create a statement in that format.
A statement for a pass-thru fund might only have Interest. Statements might have different language or terminology. You might have different styles for different divisions.
Regardless of the reason, the merge document created will point to a different data set so that when merged each fund will have the correct style.
When you initially set up the statement styles, you must remember to create one merge document for each of the data files.