I've been having this problem in DOSBox for as long as I remember, since version 0.73 at least. Basically the problem is this: when several sound samples are played simultaneously, some of them are skipped, as if there are not enough sound channels. The best example in these games is placing a building on the map. Two distinct simultaneous sounds are used for this action - "thump" sound of placing the building and mechanical "deployment" sound. More often than not only either one of them can be heard while correct behaviour is that both should be heard.
This doesn't occur in PCEm and Retroarch DOSBox-pure core, so I guess it's something standalone DOSBox specific. The problem is present in the latest Windows builds and also occurs in most recent SVN, ECE and staging builds as well.
I haven't checked the linux version though, don't have linux installed at this time.