This is not a very big issue if you have correctly identified the problem. The problem is more about what you should focus on in Norwegian. It is so different to itself, so Norwegians in general are used to hearing a wide range of dialects and accents. For a learner the question is which Norwegian to learn to talk in, not really how you pronounce your “Scandinavian”. If I were you I´d just speak scandinavian words in a neutral accent if you just want to be understood. If you have been in the countries (I went to Roskilde festival a lot) you see how they talk to each other. They do not understand every single thing if they don´t make adjustments to their word selection/accent, they often ask for clarification and some even switch to English.
Classe Ekman - Utrikeskorre i Oslo (Robert Gustafson) you see this kind of situation made fun of here.
If you want to speak in a “passable” manner in each language it isn´t impossible (Frank Von Helvete as Cornelis Vreeswijk, Mads Mikkelsen speaks fluent Swedish, David Dencik, Iben Hjejle) but it is far easier for Danes to pronounce Swedish and Norwegian, so you are already in a better position. Some Norwegians sound Danish, a friend of mine from Roskilde went to Bergen to live there and was walking with a guy for a few hours and then said “Which town in Denmark to you come from?” and he said “I am Norwegian”. I think probably more what is happening is you´re just pronouncing a word wrong or saying it in a way that confuses them as they aren´t sure what language to expect. Norwegians don´t understand Danish people very well, just better than Swedes can. Danes don´t understand all Danes, especially from Jutland to Zealand.
In my opinion, in order to really understand the differences between the language you need to learn them from a children´s point up, as literally most adults can just speak to each other in modified versions of their languages and get by fine. Read Norwegian children´s encyclopedias and young literature, and watch and listen to kid´s shows, this is where the differences will be more pronounced. Children from Scandinavian languages are not often competent in the other language (Norwegians do tend to watch a lot of Swedish kid´s TV though). In one of the Språket podcasts, one of the Swedes living in Norway said he actually hates Norwegians speaking “svorsk”, essentially Norwegian with the words changed wrongly to Swedish, because he thinks the Norwegians sound stupid when they do this as they think they are really speaking Swedish, but for him it is like the French accent from Allo Allo being considered “French”.
To build your skills, there are three language podcasts listening to, Språket from Sveriges Radio, Klog på Sprog on DR and Språksnakk on NRK. If you listen to these podcasts regularly they often mention the differences between the three languages and misunderstandings that exist.
Språket - alla avsnitt | Sveriges Radio - quite a few episodes about Scandinavian dialects, Norwegian and Danish.
Språket - Gör som Skavlan - snakke svorsk! - Podcast - particular pod about a famous TV show house Skavlan, his shows are on youtube as well very funny to watch the Scandinavians talking to each other.
Good shows:
“Ett språk är en dialekt med en armé och en flotta” | Språket | Sveriges Radio
Gurka på svenska och agurk på norska, hur är det möjligt? | Språket | Sveriges Radio
Vent, jeg skal bare hente Noora sin sykkel | Språket | Sveriges Radio
Vad är skillnaden på en dialekt och ett språk? | Språket | Sveriges Radio
Norska + danska + svenska = sant | Språket | Sveriges Radio
Norsken, svensken och dansken - alla avsnitt | Sveriges Radio regular show on SR