According to this article the EU Council Presidency decided to force software patents through the Council against objections from at least Portugal, Denmark, Poland and Cyprus despite the fact that discussion of a point as a B-item according to the EU Councils Rules of Procedure can only be rejected by a majority of the Council, and not by the EU Presidency.
See also this BBC News article
This decision by the Luxembourg EU Presidency makes a complete mockery out of the idea of a democratic EU, after the EU Commission earlier decided to overrule the directly elected parliament and leave the decision to the Council. Now the Council have in effect seen it's Presidency blatantly ignore the Councils own rules in order to stop dissent and prevent an embarrassing defeat for the Commission.
Unless there's some way of fighting this Council decision, the remaining chance now is that the Parliament will revolt against this undemocratic and arrogant move and refuse to approve the draft directive on second reading. However that is an uphill battle considering that an absolute majority of ALL MEP's is needed, and a significant number of MEP's usually won't attend every sitting.