I wish I could tell you that it won't affect you, but it will. At several companies I worked for I, as a hiring manager, wouldn't even get to see your resume or

I wish I could tell you that it won't affect you, but it will. At several companies I worked for I, as a hiring manager, wouldn't even get to see your resume or application if the suspect company was a recent (< 5 years) employer, you'd be filtered out by software, recruiting and H/R. If there's an active criminal investigation involving the company, you'll be suspect, fairly or not. If you're looking to leave, I'd recommend finding direct connections in candidate companies who could "sponsor" you through their H/R filtering systems, just so you get a chance to get an interview without the bias of whatever's going on at your current company.