Two companies that write software for big mainframe computers came down with a case of the "Big Blues" Wednesday.

Shares of

Computer Associates

(CA) - Get Report

and

BMC Software

(BMCS)

both plunged, hitting 52-week lows, after the companies warned of earnings shortfalls. Computer Associates and BMC, which make software that manages

IBM's

(IBM) - Get Report

big mainframe computers, both fingered uncertainty over the pricing and the design of IBM's newest operating system for their woes.

Islandia, N.Y.-based Computer Associates, the third-largest software maker in the world, was the top percentage loser on the

NYSE

and the Big Board's most actively traded issue as it fell 22 1/4, or 44%, to 28 7/8. Houston-based BMC fared little better, tumbling 13 13/16, or 39%, to 21 11/16. IBM took a hit as well, falling 8 1/8, or 7%, to 101 3/8.

No Relief

On the next version of its S/390 mainframe computer, IBM may change the pricing structure and possibly the design, industry analysts say. This uncertainty prevented Computer Associates from closing an undisclosed number of deals in the $50 million range, said Sanjay Kumar, the company's president and chief operating officer. IBM declined to comment on questions about the S/390.

Until IBM's precise strategy becomes clear, the stocks of both companies could remain under pressure, says Robert M. Johnson, an analyst with

ABN Amro

who is maintaining his buy ratings on both Computer Associates and BMC Software. Several other analysts downgraded the stocks of both companies on Wednesday.

The new IBM product isn't expected to be available before September, and rumors are circulating that IBM won't release it until December, analysts say. Lingering uncertainty could continue to hamper sales and profits at both companies, Johnson says. The most specific time frame IBM has offered for the new product is sometime in the second half of the year.

Late Night Warnings

Late July 3, well after Wall Street had gone home for Tuesday's Independence Day holiday, Computer Associates issued a statement disclosing that fiscal first-quarter results would miss Wall Street estimates. The company said it would report revenue of $1.25 billion to $1.3 billion, some $300 million to $350 million short of the $1.6 billion projected by many analysts.

The company elaborated in a conference call with analysts Wednesday morning, saying it expects quarterly earnings to come in at 26 to 31 cents a share, well short of the 55 cents expected by analysts surveyed by

First Call/Thomson Financial

.

"The larger deals probably had the greatest impact because they were tied to S/390," Kumar said of the software used to operate the popular IBM mainframe. "My gut feeling is we're not alone in this issue."

BMC Software confirmed that suspicion when it announced Wednesday morning that it expects earnings of 18 cents to 21 cents a share. Analysts surveyed by First Call/Thomson Financial had projected earnings of 46 cents per share.

"When you're buying $50 million worth of stuff, you might say, Let's wait a minute," analyst Johnson says. ABN-Amro hasn't underwritten for either company.

Computer Associates said first-quarter results were also hurt by a delay in closing deals that were expected to close by the end of the quarter, and sluggish European sales. The company announced some management changes meant to improve its European sales performance.