He..He , yes we have been here before
Example:
On my HP 3458A i have to send : END ALWAYS , as the first command in order to get the meter to set EOI along with the last byte sent.
If i don't, the linux gpib always times out before returning any data , and some data are lost.
Try to see what it says in the manual.
On some older HP's, EOI was selected on the "gpib addr" dipswitch on the back.
If you can get your instrumnt to set the EOI line when sending last byte , that's the 99.9% easiest way to signal "End of Data" to linux-gpib.
/Bingo