The treatment for tax gain/loss is different between individual and Corp. If Corp has a net profit, i.e., income exceeds expenses including salary, the capital gain is taxed in the same manner as ordinary income, except that, for taxable years where the corp is sjubject to tax at a rate in excess of 35%, an alternative tax applies for qulified timer gains, see section 1201(b).
Section 1231 transactions are treated as capital, subject to a recap rule in section 1231(c). Conversely, where losses exceed gains, all section 1231 transactions are treated as ordinary. This does not conflict with the above.
Inet-Fan, please let us know if you have any answers from your CPA. Thanks.