The end of communism was surprisingly peaceful. Yugoslavia rapidly disintegrating afterwards was an entirely different affair. Austria had a border with Yugoslavia - with the part that today is known as Slowenia. The actual independence war of Slovenia lasted only 10 days [1]. Still, troop movements happened in sight of the Austrian border and the Austrians were not happy at all.
The outbreak of full conflict between the recently declared independent states of Croatia and Bosnia with Yugoslavia happend shortly after and was not over in 1993/94 [2]. So I guess any Austrian border patrol would have been wary of refugees/smugglers/shady elements crossing any eastern border.
Hungary was never immediately affected by the war in the former Yugoslavia, but it had an enormously long border with a country at war with itself and the economic impact (loss of trade with the southern neighbours, influx of refugees etc.) could be felt in many ways. So, compared to western standards, Hungary might, at the time, have looked slightly less than appealing. In particular if you didn't know the local language and were smuggling...
[1] http://en.wikipedia.org/wiki/Ten-Day_War [2] http://en.wikipedia.org/wiki/Yugoslav_Wars