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Software supplier Amaze, one of the firms named by BSA, said it was disappointed to have been singled out, given its "full co-operation" with the anti-piracy body.
BSA, which represents companies such as Microsoft, Adobe and Symantec, has been naming-and-shaming for 18 months, even if companies have reached financial settlements.
Legal experts and user bodies have urged extreme caution when dealing with the BSA, which has sought to audit software from any company with more than 20 staff.
The latest named miscreants were Amaze, which paid £52,000, and Comojo Holdings which paid an undisclosed amount.
Stuart Melhuish, chief executive officer of Amaze, admitted that the company did find a licence shortfall this year following a period of significant expansion. But as soon as it was approached by the BSA Amaze made a "frank and open declaration and fully co-operated" with the organisation. It bought licences and amended operating procedures to ensure conformance, Melhuish said.
"We are disappointed, having taken these measures that, of the 6,500 companies in Europe subject to enforcement actions in the past year, the BSA have chosen to single out Amaze," he said.
Mike Newton, UK programme manager for the BSA, said, "If companies come to us with a problem, we will not prosecute."