this is my first post on here. If I am violating any rules, I apologize in advance. Also, if you see a simple way I can improve my conventions for coding
Welcome, and no worries, for a first post it's fine :-) Some good introductory reading is PerlMonks for the Absolute Beginner, The Perl Monks Guide to the Monastery, and How do I post a question effectively?
Sorry, I can't reproduce the issue, neither with your original code with strict turned off, or with it turned on and the appropriate my declarations added (although I'm not surprised by the latter). Without seeing more code (a representative Short, Self-Contained, Correct Example), I can only guess: Either you're making a mistake somewhere in the "manipulations occur here producing a new array with 6 values", which you haven't shown us, or, since you're apparently not using strict, meaning all of those variables are global, there is some "cross-contamination" happening between the arrays (Update 2: I just wrote some more on that here). This is one reason you should always Use strict and warnings*, since it helps enforce proper scoping of your variables!
* Update: Your program should begin with this, see the Basic debugging checklist: