Source references other queries or steps, so it may not directly access a data source

I'm sorry if i was not clear. When hard-coding the values as you show in your example it works.

However, this is not how the parameter is set up, nor is it the desired behavior. 

First I make a call to the SQL Server database used by all of the queries

let
Source = Sql.Database(DBServer, JIRA_Database, [Query="

SELECT jira_proj_dwkey
, jira_proj_name
, jira_proj_category_name
, jira_proj_key_cd
, product_owner_name
, CASE
WHEN proj_active_indicator='Y'
THEN -1
ELSE 0
END jira_proj_active_flg
, created_dt
FROM dbo.dim_jira_proj
WHERE jira_proj_dwkey > 0
"])
in
Source

Knowing that linking directly to a result sometimes causes a problem, I create one referencing the SQL call named JIRA_Project_fmSQL.

let
Source = JIRA_Projects_SQLLib
in
Source

This creates the table RELATION_TABLE_Project_Information based upon a join of the user's entered data (USERTABLE_BaseProjectInformation) and the data returned from the project information pulled from SQL Server.

I cannot use the simple thing you posted as the user table contains additional information such as the project name, the manager, the start date of tracking, etc. 

let
Source = USERTABLE_BaseProjectInformation,
#"Merge JIRA data table" = Table.NestedJoin(Source, {"jira_proj_key_cd"}, JIRA_Projects_fmSQL, {"jira_proj_key_cd"}, "JIRA_Projects_SQLLib", JoinKind.LeftOuter),
#"Expand JIRA Project Key and Full Name" = Table.ExpandTableColumn(#"Merge JIRA data table", "JIRA_Projects_SQLLib", {"jira_proj_dwkey", "jira_proj_name"}, {"jira_proj_dwkey", "jira_proj_name"})
in
#"Expand JIRA Project Key and Full Name"

Using that result, I create the parameter list.

let
Source = RELATION_TABLE_Project_Information,
#"Filter to Software Projects" = Table.SelectRows(Source, each ([jira_proj_methodology_type] = "Scrum" or [jira_proj_methodology_type] = "Kanban")),
#"Removed Other Columns" = Table.SelectColumns(#"Filter to Software Projects",{"jira_proj_dwkey"}),
#"Removed Duplicates" = Table.Distinct(#"Removed Other Columns"),
#"Changed Type" = Table.TransformColumnTypes(#"Removed Duplicates",{{"jira_proj_dwkey", type text}}),
#"CreateList" = Text.Combine(#"Changed Type"[jira_proj_dwkey], ",")
in
#"CreateList"

If I use this parameter in a SQL statement, it throws the exception.