For my understanding,

"Your Box 13 was unchecked" is right . it is not as what you thought it was wrong because althought you participated,  you did not contribute any money yourself which means actually you did not get any benefit from that participation in retirement plan.and all your money in your W-2 are all taxable, no any deferred. YOu can see that all the boxes  taxable wages, social security, and medicare wage are the same if ur salary is not high(106800)...

ok just go ahead to set up IRA. no problem.