My experience, based on a rather small sample, is that there is a strong overlap between being on the Spectrum and having at least some doubts about ones gender identity. Possibly our lack of social awareness (= tact) means we are more ready to admit to something that most people would keep well hidden. Possibly there is a real correlation.
At one point I found that of the four male Aspies regularly posting to a small forum, three had well developed female personas. Too small a sample, but interesting. Another forum member was a paintball ref and really one of the lads (and female).
Anyone else willing to speak for themselves? Any parents noticed boyish girls or girlish boys?
I have worked with many people with ASD who have expressed concern about their self-identity in general - people have told me, for example, how they have "adopted" various interests, mannerisms, & clothing styles from imitating those around them. Sometimes they have "switched" identities quite abruptly.
I have seen several young people with ASD who have shown & expressed definite "gender dysphoria", & who have received some assistance with this via their local Child & Adolescent Mental Health Services (CAMHS). One boy had a long-standing interest in female pop singers, which had extended into dressing up, & then into expressing more general dissatisfaction with being male.
A Dutch study published earlier this year of around 200 young people referred to a Gender Identity Disorder (GID) clinic found 8% had co-occurring ASD, so there is some research evidence to support a link between the two.