I am having similar problems. On the first layer too much filament is extruded so I turn the flowrate down to between 50 and 70% in repetier. I then turn it back up to 100% when it isn't extruding enough filament (usually in layers 1 to 4)
I also set it to do only 1 solid layer on the top and bottom.
I have found that setting the infill to less than 1, i.e. 0.9 or 0.8, doesn't extrude too much filament but is still 'solid'.
I am using slic3r 0.9.9 too. I think it's still a little buggy.
For your reference, here is my config file for solid at 0.3mm layer height. At least I think it is, slicer wont seem to let me export configs 
Post's attachmentsSolidoodle 0.3mm.ini 2.76 kb, 8 downloads since 2013-05-31
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Industrial Designer
Fresh Design Works (UK)
www.freshdesignworks.co.uk