“I billed as this corporation, deposited all the checks into this account and paid myself as an employee with a W-2 at the end.“----->As you said, if you are billing as 1099 or corp-to-corp and acting like an employee, you can get penalized big time by the IRS.
“However, they apparently filed a 1099 with the government and now the IRS wants me to pay taxes against that. I'm not sure how to proceed”------>In principle, the Form 1099-MISC is NOT REQUIRED if the work or services rendered is between corporations. 1099 forms are only required to be sent if the payments are being made to independent contractors who are not formally established as a corporation. That is what is meant by corp-to-corp. However, technically, a corp-to-corp arrangement also often receives a 1099 so it's more accurate to call "1099" self-employed or schedule-C , as you can see,sch C of 1040 is where one reports self employed earned income for which they did not receive a W2; if you work C2C and the customer then sends you a 1099, you could have big issues at tax time. When you work C2C, then your customer is not required to send you a 1099-Misc at tax season as some usually do.However, in the case of S corp, if the 1099 is in your name , NOT in your S-Corp name. No problems .You just give it to your tax preparer. Since you billed and were paid on your personal name, then you will have to pay taxes when you file your 1040. If it is in your personal name and you billed on your S corp name and were paid on your S-Corp name, you need to have them change the name of recepient on the 1099.
“- I think I'm needing a new tax accountant”---> I guess so.