Pitch is represented by timing, in other words, middle c is 256 hz or 256 cycles per second a above middle c is 440 cycles per second.
If you slow the cycles per second of a note played at a at 440 cycles per second down to 256 cycles per second it will sound exactly like a c.
A correct pitch then produced by a computer is dependent upon the speed that the computer operates at.
If the computer runs slow the pitches will all be flat.
I have done some work many years ago in the area of computer basic operations and the speed of internal clock operations in computers.
What I would say is, the speed of the computer governs the pitches the computer plays in exactly the same way that slowing down a vinyl record lowers the pitch or a train hooter sounding as it moves away lowers the pitch.
Computers are run at whatever speed the system board clock cycle allows them to run at and this may vary and can affect the speeds that software programs run at and the pitches they produce.
Computers cannot be relied upon to govern speeds correctly they run faster or slower depending upon hardware and software resource usage.
The only computer systems that can be relied upon for correct and consistent speed of operation are real time systems that control traffic lights aerospace and flight systems. We dont have access to those real time systems they are very expensive.
The only caveat to this is if the computer is configured with a separate clock system external to the system board such as a timing chip on a separate device, or an external clock maintained and accessible over an external interface such as an internet timer clock.
Even if there is a clock governing the absolute time for pitches, if the computer suffers timing issues the pitches the computer generates must suffer.
One such internet timer clock is the world clock but that is not generally useful for timing a computer internally down to microseconds, and it is not useful to try to do this.
I am not at all surprised that inconsistent pitches in music played by computer systems has been seen, what I am surprised at is that these effects are noticed so little,
For example a music score played over an internet connection depends upon the packets delivered over an internet contended link. If the packets are delivered too slow the pitches may be affected, or pauses appear.
This means musical phrases are sliced up into parts and then reassembled in the computer, and if there is lots of traffic over the internet then slowdowns brownouts and dropouts are inevitable.
A router might receive 350,000 packets per second so pitches at 256 or 440 cycles per second are sliced up into fragments of cycles and each one must be assembled in the correct order or the pitch is corrupted in some way.
We cannot expect music to keep correct time there are too many variables, we cannot expect computers to even play a cd or a dvd or internet music correctly, it is simply not the way computers are designed to operate.
Typically modern computers have enough resources available to not run out while we listen to music so we dont see these effects but there is still a risk of that happening.
I cannot explain the symptoms described there are too many factors at play, it may be due to a temporary loss of of resources preventing correct timing of a short duration that then cleared itself when whatever consumed the resources stopped acting, then the software could operate correctly once more.
It could be that the software running had a corruption and that surfaced as a slowdown.
Resource loss is the usual culprit for slowdown and stagnation it being fairly common for a bad program to consume 100% of the computers resources and nothing is then left for music programs to use.
Expect to see this problem re surface occasionally.
My background credentials are in computer technical support, systems building, and systems troubleshooting on all platforms from intel to motorola to sun unix plus tcpip comms and ethernet.