Almost certainly, at least once.
It is a mistake to think of the NSA merely as a SIGINT (signals intelligence) operation. They also do defense, especially at the Information Assurance Directorate (IAD), as seen on this link to the NSA:
IAD has developed partnerships with government, industry, and academia
in order to commercialize Information Assurance (IA) technology and
products. By setting standards and encouraging vendors to build to
those standards, IA ensures that secure devices and networks are not
only available to customers, but keep pace with current technologies.
What is information assurance (IA)?
IA identifies and corrects security vulnerabilities before our
adversaries exploit them...
In 2011, the Cybersecurity Operations Center (this links to the NSA) was created.
The Cybersecurity Collaboration Center is NSA’s groundbreaking hub for
engagement with the private sector. These partnerships help NSA to
prevent and eradicate foreign cyber threats to National Security
Systems (NSS), the Department of Defense (DoD), and the Defense
Industrial Base (DIB).
On this page, the CCC describes its job, and among the points is this:
Develop guidance and technologies [boldface mine] to improve the security and
capabilities of cross domain solutions
The case in point--that shows what must have been NSA involvement--is the identification and elimination of a weakness in the Secure Hash Standard (SHS).
On July 11, 1994, the NIST proposed an interesting revision to FIPS 180, about the Secure Hash Standard:
A revision of Federal Information Processing Standard (FIPS) 180,
Secure Hash Standard (SHS), is being proposed. This proposed revision
corrects a technical flaw that made the standard less secure than had
been thought. The algorithm is still reliable as a security mechanism,
but [sic] the correction returns the SHS to the original level of
security.
FIPS PUB 180-1 it explains:
A circular left shift operation has been added to the specifications
in section 7, line b, page 9 of FIPS 180 and its equivalent in section
8, line c, page 10 of FIPS180. This revision improves the security
provided by this standard. The SHA-1 is based on principles similar to
those used by Professor Ronald L. Rivest of MIT when designing the MD4
message digest algorithm 1, and is closely modelled [sic] after that
algorithm.
NSA surely had a hand in this, and it was likely done to protect users (or was it?). Given the mandated roles of the IAD and CCC, and especially that the CCC develops technologies, it is reasonable to conclude that these technologies are sometimes shared--in order to protect U.S. critical infrastructure and correct security vulnerabilities. As far as the question goes, about strengthening algorithms, there is at least this one instance that we know about since it is unclassified.
