Just as Peregrine Systems Inc. hammered out its acquisition of Harbinger Corp., the Nasdaq started its painful plunge, making the stock-for-stock deal seem more and more expensive as the days wore on.

By the time the deal was announced on April 5, Peregrine’s stock had dropped from a high of more than $90 in February to $58 per share while Harbinger’s stock landed at $24 from a March high of $37. And with Peregrine paying three-quarters of a share of stock for each of Harbinger’s shares, many investors complained the San Diego infrastructure company was paying far too much for the Atlanta-based maker of e-commerce enabling software.