If an OPT student at the start of OPT, is on bench for more than 3 months without any payroll, then Can it create problem at the time of OPT extension?
You just need to get employed within 90 days of when ur OPT starts. Your first OPT can be a volunteer job in a company without pay. You need not have pay checks. But when you apply for OPT extension you cannot be on volunteer job without pay. You need to be paid during the extension period.
Coming back to your question, not being paid during the first three months of your OPT will not afffect you extension process.