Like I stated already, referring to the line(s) you are pasting which are longer that others, once CR/ENTER is processed it takes longer than a normal keystroke to process on the emulated computer side and the PASTE UI function doesn't afford the time needed for this processing (i.e is blindly spitting out whatever is in the buffer). This leaves you with missing characters (in this case, the next line misses a number at the beginning of the next line number). You can adjust the text pasted to insert maybe a couple line feeds or additional spaces to allow time for the computer(s) to catch up to the paste, maybe?
I used to have quite a lengthy report on this function back when BugZilla used to host Mess bugs - just haven't made the same thing for MAMETesters yet (looks like I should).
I can't explain the basic size differences when compared to other emulators. I used "mess64 sc3000 basic3a" (title from softlist) and was given 26620 bytes free: