As long as the EIN on your W-2 matches the EIN you are entering (or importing), this difference in the name won't affect your tax return.
It is not uncommon for the employer's "official name" (the one showing on their EIN account) to be different from the one on the W-2s they send out. The name they used to apply for an EIN may be different from the name they "do business as" (DBA), to include what name they have entered in their payroll system.
