They were originally designed to stack. The normal CR is the total number of levels a character has, inherited template stack first then classes and followed acquired templates. Thats how you get the Effective Character Levels, its the same as cross-classing when adding your levels.
What HeroLab is showing seems correct... it is somewhat amazing that it is, given how outside the expectations for Pathfinder the particular PC is. It sounds as if you are unaware that Pathfinder has dropped or replaced some of the concepts of D&D 3.x, and you are expecting to see them still supported "as they were".
What follows is a somewhat pedantic look at what's different; feel free to ignore it
Pathfinder is based on D&D 3.5, and you can fairly easily use a class or monster from the 3.x sources in your Pathfinder games.. on paper. But since the release of the Pathfinder game rules, Pathfinder has slowly but surely evolved away from the 3.5 base. Some concepts, like Effective Character Level and Level Adjustments, were dropped entirely or replaced. In other cases, the rules published by Wizards of the Coast were not "Open Content" and
could not be used in Pathfinder for legal reasons (such as Monster Classes from Savage Species).
The Pathfinder core rules cover up to level/CR 20. Adventure paths end at about level 16-17 partially because that puts the final bosses at CR 20 or so... the end of the range that the core rules cover.
Epic Handbook rules could be used with Pathfinder as a house-rules type of decision, but Paizo ultimately was not happy with them and added the Mythic content. That pushed the supported CR for monsters up to 30 (demigods). Characters are still leveled 1-20, with the addition of Mythic abilities on the side.
If/when Paizo decides to add statistics for true gods (beyond demigods) to the system, the supported character level may rise, or they may take an approach like Mythic and have more power "on the side".
TL;DR 1: Long story short, a character with nearly 60 class levels is way out into house rules territory in Pathfinder.
Also, Challenge Rating (CR) is
not equivalent to Effective Character Level (ECL). CR is a measure of how much of a challenge a creature is to a party of four adventurers; it specifies the Average Party Level (APL) of a four-person party that the creature is a suitable opponent for as an "even" challenge. The CR of a PC is level -1, or -2 if the character has NPC class levels.
For unusually powerful races, if the GM wishes to use them, the recommendation is to treat their CR as their level and give the other PCs additional levels to even them out. This does not apply to monster races where the balance is "even enough", or where the monster is on the weak side.
The Advanced Race Guide introduced rules for creating new races, by assigning costs and ranking to racial abilities. Within this framework, the impact of a PC with higher-than-normal racial abilities is not based on it individually, but on how the party as a whole is put together, raising the APL of the party to compensate for having stronger-than-normal members.
I don't see any place in the rules where characters with Templates are supported. In Pathfinder, such characters "should be" re-built using the Advanced Race Guide's Race Builder to determine the overall power in terms of Race Points.
TL;DR 2: Templated races are not supported in Pathfinder, generally, so this is also very much house rules territory.