"We were aware a limited number of users were experiencing that issue, and we were able to address it," said Zune spokeswoman Katy Asher.
The software maker hadto have the update by midmonth, but the patch took slightly to develop and test.
In addition to addressing the song-skipping issue, the Zune 1.3 software update aims to offer quicker syncing and improve a situation where the Zune's battery could drain more quickly after using the FM tuner.
Microsoft also noted that the Zune held its No. 2 spot in NPD's February retail sales figures, though its share of the hard drive-based music player market dipped to 8.8 percent from 9.9 percent a month earlier.
"We're still happy with where we're at," Asher said, noting the company's strategy is a long-term one not focused on month-to-month fluctuations.
Microsoft released a Zune update in December, making the device and its desktop software.