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I presume this is a profit sharing arrangement that you have with the employer.
I do not think it matters since if the amount that was given to you in the first check as W=2 wages would have been given to you in Form 1099 than you would owe taxes of 15.3% appx. However,since it was given to you as W-2 wages the employer paid 7.65% of FICA and medicare and 7.65% came out of your paycheck. Hence the employer took a reimbursement of 7.65% from the second check that he gave you.
For eg. Say the first check was for $1000 - $76.5 from this amount was deducted for FICA and medicare and the net check of $923.50 was given to you. However, the employer also paid $76.50 in fica medicare as employer share since the amount was reported on W-2.
In the next profit sharing check the employer gave you Form 1099 income of $1000 but took out $76.5 which the employer had paid and gave you a check of $923.50.
Now since the first check is on W-2 - you have already paid the FICA and medicare and hence you would not owe these taxes again.
On the second check you will owe FICA and medicare tax upto 15.3%.
So overall you will end up with the same amount.
From first check $ 1000-$76.5(deduced from payroll) - $76.5 (deducted from the second check)
and from the second check $1000 - 15.3% appx. FICA and medicare tax due to IRS.
Let me know if you have any question.
Please note: This advice is provided with the understanding that all the relevant facts have been provided by you. Any change in facts might affect the advice given and hence may not be relied on in such cases. Nothing contained in this reply was intended or written to be used, can be used by any taxpayer, or may be relied upon or used by any taxpayer for the purposes of avoiding penalties that may be imposed on the taxpayer under the Internal Revenue Code of 1986, as amended.