I haven't got a great deal of time to investigate this right now, but it appears that when CSS is being combined/minified, @import is not causing the imported files to be included.

I'm using the default configuration, with the only changes made being adding my specific JS/CSS resources, and changes to defaultDebugEnabled and defaultIgnorePipelineWhenDebug.

I was including the CSS resource

<resource path="~/Content/themes/base/jquery.ui.all.css" />

jquery.ui.all.css simply contains

@import "jquery.ui.base.css";
@import "jquery.ui.theme.css";

jquery.ui.base.css simply contains

@import url("jquery.ui.core.css");
@import url("jquery.ui.resizable.css");
@import url("jquery.ui.selectable.css");
@import url("jquery.ui.accordion.css");
@import url("jquery.ui.autocomplete.css");
@import url("jquery.ui.button.css");
@import url("jquery.ui.dialog.css");
@import url("jquery.ui.slider.css");
@import url("jquery.ui.tabs.css");
@import url("jquery.ui.datepicker.css");
@import url("jquery.ui.progressbar.css");

When the pipeline was being invoked, the contents of at least some of the imported CSS files was not being rendered. I searched the rendered CSS for the selector .ui-helper-hidden that occurs in jquery.ui.core.css, and it wasn't present in the rendered code. When I turned off the pipeline, the files were all included correctly and my jQuery UI content was formatted correctly.

I've worked around this issue by directly referencing the files imported by jquery.ui.core.css in combres.xml (in the process excluding some unused CSS files :-).

Btw, thanks for a great tool.