Вопрос: Совместимы ли коммутаторы D-Link и Cisco по протоколу MSTP?

Ответ: 

Совместимы. Но для того, чтобы, при настройке MSTP (802.1s), не возникало проблем следует обновить Cisco IOS до версии 12.2(25)SEC или более поздней.

Подробная информация содержится здесь:

Release Notes for the Catalyst 3750, 3560, 2970, and 2960 Switches, Cisco IOS Release 12.2(35)SE and later

In Cisco IOS Release 12.2(25)SEC for the Catalyst 3750, 3560, and 2970 switches andin Cisco
IOS Release 12.2(25)SED for the Catalyst 2960 switch, the implementation for multiple spanning tree (MST) changed from the previous release.
Multiple STP (MSTP) complies with the IEEE 802.1s standard.
Previous MSTP implementations were based on a draft of the IEEE 802.1s standard.

смотреть подробней

ciscos implementation of MST with IOS 12.2(25)SEC is based on the ieee 802.1s standard.
cisco implementations of MST on previous IOS versions are 'prestandard'.
perhaps you should consider upgrading your IOS to 12.2(25)SEC or higher.