The OP is not talking about putting in money for people not yet eligible, but making a true-up as soon as they enter the plan. For example:
Flyboyjohn enters the plan on July 1. He's making $2,500 semi-monthly. Should the company make his first SH contribution $75 (2,500 * .03) or $950 (2,500 * 12 + $75)?
I would say they can wait until the end of the year. Or do it right away. As long as it's consistent.