Septated Cyst / Protein in Urine

I am doing some research for my wife who has recently received some troublesome findings.  An ultrasound of the uterus found it to be nongravid and otherwise unremarkable. Ovaries were found to be of normal size, however a 1.6 cm septated cyst was seen in the right ovary and a tiny cyst was present on the left.  The appearance was non typical for polycistic ovaries and no other abnormality was seen.  Her blood work showed her FSH to be at 7, Testosterone at 1.8, and Progesterone at 3.4, Estradiol at 96, Glucose Serum Fasting at 4.4, Cholesterol at 5.31, LDL at 3.38...Her Urinalysys detected .5 Ketones (mmol/L), Protein at 1.0 g/L and Trace Leukocyte...
Her doctor wants to send her for another ultrasound in about 2 months..
How concerned should she be about the septated cyst, such as it's size and the fact that it is septated?  Her urinalysis also seems to be concerning, since the Protein and the Ketones were found.  She has missed her periods for close to up to 1 year at a time...Her Gynecologist has put her on Progesterone Herbal Cream in the past and also Estrogen.  A previous ultrasound showed findings of small cysts and we were wondering at the time if it was Polycystic Ovarian Disease, however the most recent ultrasound found two cysts only...
She is 36 years old and has never had any children...
She also has Scleroderma...

How concerned should we be about her most recent findings?
Thanks for your help.

[MickeyVicki]

Your wife's autoimmune condition might be affecting her kidneys, blood vessels, and possibly her liver, and could be causing these results.  I think that the scleroderma site (http://www.srfcure.org/srf/home.htm) has a question forum and perhaps someone there can help you.  I personally have 'high' (inasmuch as the results should be about zero) ketone levels if my urine sample is taken while fasting.  

As for the cysts..well...if  you have read the other posts on this page, then you have an idea of what tests and procedures are likely to occur if the cysts do not resolve on their own.