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The anti-piracy organisation, which represents companies such as Microsoft, Adobe and Symantec, has pursued a policy of publishing details of non-compliant organisations, even if companies have agreed financial settlements.
The policy has prompted legal experts and user bodies to urge companies to use extreme caution when dealing with the BSA.
The BSA said Clackmannanshire Council bought 470 loose-end user licence agreements from an independent supplier, over and above its select agreement with Microsoft. Loose-end user licence agreements are invalid when sold separately from a software package, and are therefore illegal.
Mike Newton, programme manager at the BSA, said organisations which find they possess illegal software should not bury their heads in the sand.
"Unfortunately, Clackmannanshire Council persistently refused to co-operate with either Microsoft or the BSA to rectify the situation," he said. "As a result, the BSA was left with no alternative but to instigate proceedings against it."