I usually publish to pdf using pdfx1a option and this normally sorts any transperancy and lens issues when doing litho artwork, always flatten completely for digital though or if importing into another programme (including Draw)
Bleed – if publishing to pdf
settings – Pre press tab – tick bleed and set required amount
If printing to cutepdf (or similar)
Print – layout – tick bleed limit and set required amount
Export to EPS – advanced tab – Bounding box PAGE – tick bleed limit and set required amount.
I have found that many trade printers prefer pdfx1a but eps seems better for many digital rips that said alot of trade printers put your files into their programme of choice for batching purposes and this is where the problems seem to start so the flatter the file – the more reliable it is for everybody
Alan d