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As one who has used Sigil nearly from the beginning, I've been very impressed with recent version - it's far more enjoyable to use, and far less quirky and more robust than the earlier versions.
I find in my work, that I prefer to do most of my xhtml coding & editing in Word 2010 and UltraEdit 17 with as much error-correcting performed in these edits as possible. Then I copy/paste the file into a Sigil template epub containing no text but already containing the required css file. At this point I save the new epub with a different name and proceed to apply the finishing touches to the epub in Sigil (always with Tidy turned off!) Sigil quickly catches any xhtml errors in the imported document and I correct these errors and also correct the errors in my UltraEdit html file. Occasionally Sigil does crash but this presents no critical problems because I periodically save the file, and if a really major problem develops in the Sigil version, I can copy/paste the corrected UE17 file back into the Sigil template epub and start over in Sigil.
With this approach I've never encountered any problems such as you seem to be encountering.
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