Recently, I came across this peculiar problem. The system was taking too long to execute the subcontracting challan creation (J1IF01). The user would enter the 541 material document, press enter, and could go out for a coffee / smoke while the system would get into a seemingly endless execution. It would materialize finally, but at the cost of time and health (of the user, of course).
A quick observation in SM50 revealed that it was waiting for MSEG table with a select statement.
It was finally discovered that this is a known problem and can be solved by applying sap note 1125316. The code correction obviates reading MSEG table and reads a structure instead. This note should be applied in all CIN based systems before things go haywire.
The note also mentions that this code correction should be applied post every support package upgrade.
Aroop's notepad 