CS3 script runs slow with CS4 and CS5

I have written a table transformation script for InDesign CS3, which formats an imported Excel table.
With InDesign CS3 the script runs well. Now I tried the same script with InDesign CS4 and CS5 and it runs very slow. It's about 10 times slower than with CS3.
I tried to turn off redrawing, but this didn't help. It even got slower again!
Does someone has made similar experiences? Could you solve the performance issue?
Do scripts in CS4/CS5 generally run slower than in CS3?
Does CS4 differ so much to CS3 that the script runs 10 times slower?
What can I do to improve the execution performance?
Thanks for any tips / advices etc.

I now have made some tests with profile / timing. Here are the results.
you find the code snipped below. It iterates first over all rows and then over all cells inside of the row. In the cell iteration, the function hasGapInLineBelow(...) does more iterations.
The example is with a table of 42 rows and 9 cells.
I have compared CS3 and CS5
there are 3 test cases:
for 1/1 means: first for-loop is in iteration 1 and second for loop is in iteration 1 (statements for first row and first cell done)
for 1/9 means: first for-loop is in iteration 1 and second for loop is in iteration 9 (statements for first row and all 9 cells of the row done)
for 2/9 means: first for-loop is in iteration 2 and second for loop is in iteration 2 (statements for second row and all 9 cells of the row done)
it's strange that normal variable assignments take lot of time (like the statement startPos = indexLeftNeightbourOfCurrentCell;) -> I don't understand why this can be so time consuming!?!
it's also strange why in "for 1/9" and "for 2/9" variable assignments take much longer than in "for 1/1"...
could I use another data type than array for the variable isMergedRow? Which one?
do you know any performance optimizations?
in which time unit ExtendScript Toolkit shows the measured periods?
how are the times calculated in loops? Are these the times sumed up over all iterations or is it just the time for a single statement?

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