The software maker beat analysts consensus estimates for second-quarter non-GAAP earnings per share by two cents, hit the high end of its revenue targets, and raised its outlook for the current quarter.

But the revelation that it has added its name to the list of companies looking at stock option accounting practices, which could lead to earnings restatements, took the gloss off the otherwise rosy picture.

Our audit committee has initiated an investigation into our historical stock option granting practices, and the results of this investigation could adversely affect the financial information previously reported, CFO Mark Dentinger said in a conference call.

But, when asked, he said that the company is not currently being investigated by the Securities and Exchange Commission or attorney general.

BEA shares declined over 2% after hours. Fortunately for BEA shareholders, the stock had risen over 4% during regular trading, on the back of a favorable analyst report.

For the quarter ended July 31, the company saw its net income more or less flat at $36.3m, on revenue that was up 19% at $339.6m. Income was depressed by compliance with stock option expensing rules. Non-GAAP earnings was up 49%, and at the per-share level it was $0.14, two cents better than the consensus.

Revenue from software licenses was up 15% at $136m. Services revenue was up 22% at $203.6m.

Chief executive Alfred Chuang pointed to growth in China, India, Korea and the US federal business as the highlights of the quarter and key drivers of the software business.

He also played up the AquaLogic line of service-oriented architecture plumbing products, saying they were sold in 11 of the company’s 17 million-dollar-plus deals during the quarter. AquaLogic was over 20% of total license revenue, he said.

The older and slower-growing application server business also executed well, he said, going against some of the more pessimistic industry forecasts.

The executives said they expect third-quarter revenue of between $341m and $355m, which compares well to the Reuters analysts’ consensus estimate of $341.6m.

The key thing is we’re getting some thrust in both the license side of the business, which is on par with what we expected, but we’re also seeing a super-strong support business, and it’s the support business that is driving a good portion of the thrust in the total revenue line, Dentinger said.

While BEA investigating its options granting practices is rightfully making investors nervous, the company played down the reasons for the probe.

It’s the fashion of the Valley, to be honest, Chuang said. The audit committee felt, and the management team felt, that it was diligent on our part that we should go get an independent group to look at all this historical stuff.

The number of companies that are have said they are looking internally at options accounting, or have engaged independent auditors, or are being investigated by the feds, is approaching the 100 mark.

While there have been fraud charges charges leveled at former Silicon Valley bosses — notably the former Brocade CEO Gregory Reyes and the fugitive former Comverse CEO Jacob Alexander — some firms have launched internal probes without the existence of legal pressure.

One current tech CEO, Daniel Warmenhoven of Network Appliance Inc, which has concluded that its own options practices were all legitimate, condemned the broader SEC investigation, calling it a witch hunt, in an interview.

I thought the SEC’s role was to build investor confidence. What they’re doing right now is destroying it, and I don’t see the purpose, he told BusinessWeek. They’re penalizing today’s shareholders for events that occurred five years ago. But who is this protecting, exactly?

He noted that simply back-dating stock options was not illegal at the times many incidents were alleged to have occurred, and said that even if options had been expensed correctly, they would have not shown up on the non-GAAP results that most investors rely on to judge financial health.