Bowyer, who became permanent boss at Ewood Park over thesummer after two spells as caretaker last season, watched on as goals from Theo Robinson and James Husbands gave Paul Dickov's men the points at the Keepmoat Stadium.
However, he had issues with both efforts, claiming Robinson's first-half header was offside and branding Husband's second-half cross-shot a "fluke".
The defeat, a second in a row after losing to Nottingham Forest last weekend, might just leave him looking over his shoulder given Blackburn's trigger-happy past where they sacked three managers last season, but Bowyer is convinced things will come good.
"I think we played well with the ball, we have been camped in their half for long periods," he said of the performance.
"The first goal is clearly offside and the second goal is either an outstanding shot or a fluke, I think it's a fluke.
"So we are disappointed with the result and the manner of the goals we conceded.
"But I thought we deserved something out of the game. We are very disappointed, but I am not going to keep saying we nearly should be getting results, enough is enough.
"It's down to the quality of players to stick together and keep producing chances and keep trying to convert them.
"If you've seen us over the three games people can't fault the style of play, once we get a goal up or a refereeing decision goes our way we will see a different team.
"If you look back over the three games, the key moments are going against us and the tide will turn for us eventually."