Usually, the speaker is using those prepositions synonymously. With can also be used when you are not an employee per se, but on contract or a partner, for instance. For suggests that the speaker is thinking of the corporate body that employs him/her, while at suggests that the speaker may be thinking of the office or location as he speaks; but for all practical purposes, s/he probably intends to communicate the same fact: ' I am an employee of IBW '.
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