What steps will reproduce the problem?
1. record something.. , make sure that you have *wait comands exist
2. Change the timeouut in the options menu=>options from 30000 to 20 or 
600000
3. re run the script after changing the time out period. ( or else close 
IDE, change timeout value as mentioned in step2, load the script file 
execute it)

What is the expected output? What do you see instead?
*wait commands should wait the that mentioned in the options, it's always 
considering defautl 30000

What version of the product are you using? On what operating system?
any xp, selenium 1.0.6

Please provide any additional information below.