"Were more than a half of all Silicon Valley tech companies founded by immigrants between 1995 and 2005?" Yes, it seems so.
"Over half (52.4%) of Silicon Valley startups had one or more
immigrants as a key founder, compared with the California average of
38.8%." (p. 5)
This is, however, much higher than the average in the U.S:
In 25.3% of these companies [average of all U.S. states], at least one
key founder was foreign-born. States with an above-average rate of
immigrant-founded companies include California (39%), New Jersey
(38%), Georgia (30%), and Massachusetts (29%). Belowaverage states
include Washington (11%), Ohio (14%), North Carolina (14%), and Texas
(18%). (p.4)
The notes below probably explains the peak in Silicon Valley:
Almost 80% of immigrant-founded companies in the US were within just two
industry fields: software and innovation/manufacturing-related services. (p.4)
!Chart 6: Breakdown of Engineering and Technology Companies Founded by
Immigrants from 1995 to 2005 by Industry
While...
It is noteworthy that immigrants from China and India both constitute much less than 1%
of the total U.S. population. (p.6)
... Indians account for more than 25% of engineering and technology immigrant founders.

They also seem to have their fair share in PCT applications:
!Chart 10: Intellectual Property Contributions of U.S. Immigrant Non-citizens –
PCT Applications by Nationality – 1998 to 2006
Source:
http://sites.kauffman.org/pdf/entrep_immigrants_1_61207.pdf