Hi Pete, welcome to Interact. I own a couple of amps I bought from you a while back (Hafler and DAC).
I understand you are using
HAL's MS-2 Music Server with an external hard drive.
If a DAC doesn't have a muting circuit, then there will be popping when the DAC changes sample rate. The DAC will change sample rate to match the audio when using both ASIO and WASAPI output. With DirectSound output, all audio is resampled to one sample rate. The quality of the resampler isn't the best. I believe MediaMonkey uses DirectSound output which is why you didn't have the issue.
To eliminate popping you can go to Tools > Options > Audio > DSP & Output Format and click Output Format. Then right click one of the Outputs in the Sample Rate area. Select Set all To . . . and choose a sample rate such as 96,000 Hz. This will use JRiver's 64-bit resampler for the best quality.
You can read more out ASIO vs WASAPI in the wiki:
Audio Output ModesWhen JRiver first imports music into its library, it will analyze audio to determine peak levels, dynamic range, and set gain tags for use in volume leveling. This helps you playback songs from different albums at the same level so you won't have constantly adjust the volume during track changes. It works quite well. Anyway, the analyze audio process will increase CPU and disc activity and could cause buffering like you were experiencing.
If you still have buffering tonight, then we can check out some more things. Usually the message you received is due to not being able to pull data off the hard drive fast enough. It can happen in a network, but not usually when the hard drive is directly connected to the computer.