Maybe your web-application uses some dynamic things like sessionID. For that situations you have to modify your script. It is easy if you are using the visual navigator from QALoad 5.0 If you are useing 4.8.x then you have to change a little bit in your c-code.
Something else to consider would be using the stand alone player to validate you scripts if they are very long. Just go to QALoad~Player~Player. It is the same thig, but there is no validation timeout. I use this a alot when validating long scripts or scripts that may take a while to execute or buggy scripts.
There's an option under option/workbench/script validation that allows you to increase the timeout value for validation. By default this value is 50s which is convenient for most situation. However, it might be usefull sometimes to increase this vaue in order to prevent the workbench to abort the script after 50s